| Game Date | Conference | Road Team | Score |
| Home Team | Score | Status | Box Score | Recap | Commentary |
| National Collegiate Baseball Writers Poll |
| 4/29/2006 | * | #1 Rice | 2 | at | UCF | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #2 North Carolina | 8 | at | Duke | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Texas Tech | 3 | at | #3 Nebraska | 4 | FINAL | Box Score | Recap | 11 innings (makeup of 4/28 game) |
| 4/29/2006 | * | Texas Tech | 4 | at | #3 Nebraska | 14 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | UC Riverside | 3 | at | #4 Cal State Fullerton | 11 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #5 Georgia Tech | 4 | at | Boston College | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Cal Poly | 4 | at | #6 Oregon State | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Virginia Tech | 4 | at | #7 Clemson | 11 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Auburn | 7 | at | #8 Alabama | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #9 Texas | 5 | at | Texas A&M | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #10 Oklahoma | 11 | at | #30 Kansas | 9 | FINAL | Box Score | Recap | 10 innings (makeup of 4/28 game) |
| 4/29/2006 | * | #10 Oklahoma |
| at | #30 Kansas |
| Suspended | | Recap | suspended to 4/30, rain (1-0 OU, Top 2) |
| 4/29/2006 | * | #11 Arkansas | 4 | at | #29 Louisiana State | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Savannah State | 2 | at | #12 Florida State | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #19 Mississippi State | 7 | at | #13 South Carolina | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #14 Virginia | 8 | at | Maryland | 0 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #15 Notre Dame | 7 | at | Connecticut | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #15 Notre Dame | 7 | at | Connecticut | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #16 Arizona State | 11 | at | Stanford | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #27 Miami, Florida | 9 | at | #18 North Carolina State | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #20 Tulane | 3 | at | East Carolina | 13 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #21 Houston | 4 | at | Alabama-Birmingham | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #21 Houston | 9 | at | Alabama-Birmingham | 4 | FINAL | Box Score | Recap | moved from 4/30, impending weather |
| 4/29/2006 | * | #23 Wichita State | 14 | at | Indiana State | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Stony Brook | 3 | at | #24 Winthrop | 14 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | New Orleans | 4 | at | #25 Troy | 2 | FINAL | Box Score | Recap | moved from 4/30, impending weather |
| 4/29/2006 | * | New Orleans | 5 | at | #25 Troy | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #26 Kentucky | 11 | at | #30 Vanderbilt | 9 | FINAL | Box Score | Recap | |
| America East Conference |
| 4/29/2006 |
| Stony Brook | 3 | at | #24 Winthrop | 14 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Maine | 3 | at | Binghamton | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Maine | 1 | at | Binghamton | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Maryland-Baltimore County | 0 | at | Hartford | 1 | FINAL | Box Score | Recap | No-hitter for Eddie Bach (UMBC) |
| 4/29/2006 | * | Maryland-Baltimore County | 2 | at | Hartford | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Vermont | 8 | at | Albany | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Vermont | 11 | at | Albany | 4 | FINAL | Box Score | Recap | |
| Atlantic 10 Conference |
| 4/29/2006 | * | Dayton | 1 | at | Rhode Island | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Fordham | 7 | at | Duquesne | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | LaSalle | 1 | at | George Washington | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. Joseph's | 6 | at | Richmond | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. Louis | 4 | at | North Carolina-Charlotte | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Temple | 5 | at | Massachusetts | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Xavier | 2 | at | St. Bonaventure | 9 | FINAL | Box Score | Recap | |
| Atlantic Coast Conference |
| 4/29/2006 | * | #2 North Carolina | 8 | at | Duke | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #5 Georgia Tech | 4 | at | Boston College | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Virginia Tech | 4 | at | #7 Clemson | 11 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Savannah State | 2 | at | #12 Florida State | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #14 Virginia | 8 | at | Maryland | 0 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #27 Miami, Florida | 9 | at | #18 North Carolina State | 6 | FINAL | Box Score | Recap | |
| Atlantic Sun Conference |
| 4/29/2006 | * | Gardner-Webb | 8 | at | Lipscomb | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Gardner-Webb | 4 | at | Lipscomb | 5 | FINAL | | Recap | |
| 4/29/2006 | * | Jacksonville | 14 | at | Florida Atlantic | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Jacksonville | 8 | at | Florida Atlantic | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Kennesaw State | 6 | at | Stetson | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Mercer | 1 | at | Campbell | 12 | FINAL | Box Score | | |
| 4/29/2006 | * | North Florida | 6 | at | Belmont | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | North Florida |
| at | Belmont |
| Postponed | | Recap | PPD to 4/30, rain |
| Big 10 Conference |
| 4/29/2006 | * | Illinois | 5 | at | Minnesota | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Illinois | 5 | at | Minnesota | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Indiana | 3 | at | Penn State | 2 | FINAL | Box Score | Recap | 11 innings |
| 4/29/2006 | * | Indiana | 3 | at | Penn State | 0 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Michigan | 6 | at | Michigan State | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Michigan | 6 | at | Michigan State | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Northwestern | 9 | at | Iowa | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Purdue | 0 | at | Ohio State | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Purdue | 1 | at | Ohio State | 4 | FINAL | Box Score | Recap | |
| Big 12 Conference |
| 4/29/2006 | * | Texas Tech | 3 | at | #3 Nebraska | 4 | FINAL | Box Score | Recap | 11 innings (makeup of 4/28 game) |
| 4/29/2006 | * | Texas Tech | 4 | at | #3 Nebraska | 14 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #9 Texas | 5 | at | Texas A&M | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #10 Oklahoma | 11 | at | #30 Kansas | 9 | FINAL | Box Score | Recap | 10 innings (makeup of 4/28 game) |
| 4/29/2006 | * | #10 Oklahoma |
| at | #30 Kansas |
| Suspended | | Recap | suspended to 4/30, rain (1-0 OU, Top 2) |
| 4/29/2006 | * | Baylor | 5 | at | Missouri | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Oklahoma State | 3 | at | Kansas State | 2 | FINAL | Box Score | Recap | makeup of 4/28 game |
| 4/29/2006 | * | Oklahoma State | 2 | at | Kansas State | 1 | FINAL | Box Score | Recap | |
| Big East Conference |
| 4/29/2006 | * | #15 Notre Dame | 7 | at | Connecticut | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #15 Notre Dame | 7 | at | Connecticut | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Cincinnati | 9 | at | Louisville | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Cincinnati | 2 | at | Louisville | 14 | FINAL | Box Score | Recap | moved from 4/30, impending weather |
| 4/29/2006 | * | Georgetown | 4 | at | South Florida | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. John's | 11 | at | Rutgers | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Villanova | 6 | at | West Virginia | 7 | FINAL | Box Score | Recap | |
| Big South Conference |
| 4/29/2006 |
| Stony Brook | 3 | at | #24 Winthrop | 14 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Birmingham-Southern | 4 | at | Liberty | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Virginia Military | 4 | at | North Carolina-Asheville | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Texas-Pan American | 2 | at | Coastal Carolina | 1 | FINAL | Box Score | Recap | 11 innings |
| 4/29/2006 |
| Texas-Pan American | 7 | at | Coastal Carolina | 9 | FINAL | Box Score | Recap | |
| Big West Conference |
| 4/29/2006 | * | UC Riverside | 3 | at | #4 Cal State Fullerton | 11 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Cal Poly | 4 | at | #6 Oregon State | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Cal State Northridge | 4 | at | UC Santa Barbara | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Pacific | 5 | at | Long Beach State | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Cal Poly | 6 | vs | New Mexico | 4 | FINAL | Box Score | Recap | 10 innings (Corvallis, OR) |
| 4/29/2006 |
| UC Irvine | 4 | at | UC Davis | 2 | FINAL | Box Score | Recap | |
| Colonial Athletic Association |
| 4/29/2006 | * | Delaware | 4 | at | William and Mary | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Georgia State | 1 | at | James Madison | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Hofstra | 2 | at | George Mason | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | North Carolina-Wilmington | 2 | at | Virginia Commonwealth | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Towson | 7 | at | Northeastern | 11 | FINAL | Box Score | Recap | |
| Conference USA |
| 4/29/2006 | * | #1 Rice | 2 | at | UCF | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #20 Tulane | 3 | at | East Carolina | 13 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #21 Houston | 4 | at | Alabama-Birmingham | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #21 Houston | 9 | at | Alabama-Birmingham | 4 | FINAL | Box Score | Recap | moved from 4/30, impending weather |
| 4/29/2006 | * | Southern Mississippi | 19 | at | Marshall | 4 | FINAL | Box Score | Recap | Charleston, WV |
| 4/29/2006 |
| Arkansas-Pine Bluff |
| at | Memphis |
| Cancelled | | Recap | CCD, rain |
| Division I Independents |
| 4/29/2006 |
| Savannah State | 2 | at | #12 Florida State | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Dallas Baptist | 4 | at | Fresno State | 13 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Dallas Baptist | 3 | at | Fresno State | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Lewis-Clark State | 13 | at | Utah Valley State | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| North Dakota State | 1 | at | Valparaiso | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| North Dakota State | 2 | at | Valparaiso | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| South Dakota State |
| at | Creighton |
|
| | Recap | CCD, rain |
| 4/29/2006 |
| Texas A&M-Corpus Christi | 0 | at | New York Tech | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Texas-Pan American | 2 | at | Coastal Carolina | 1 | FINAL | Box Score | Recap | 11 innings |
| 4/29/2006 |
| Texas-Pan American | 7 | at | Coastal Carolina | 9 | FINAL | Box Score | Recap | |
| Horizon League |
| 4/29/2006 | * | Butler | 4 | at | Youngstown State | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Butler | 5 | at | Youngstown State | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Cleveland State | 1 | at | Illinois-Chicago | 12 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Cleveland State | 1 | at | Illinois-Chicago | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Wright State | 3 | at | Wisconsin-Milwaukee | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Wright State | 4 | at | Wisconsin-Milwaukee | 3 | FINAL | Box Score | Recap | |
| Ivy League |
| 4/29/2006 | * | Brown | 8 | at | Yale | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Brown | 2 | at | Yale | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Dartmouth | 1 | at | Harvard | 2 | FINAL | Box Score | Recap | 10 innings |
| 4/29/2006 | * | Dartmouth | 13 | at | Harvard | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Long Island | 2 | at | Columbia | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Long Island | 3 | at | Columbia | 8 | FINAL | Box Score | Recap | |
| Metro Atlantic Athletic Conference |
| 4/29/2006 | * | Canisius | 0 | at | LeMoyne | 6 | FINAL | Box Score | Recap | Bobby Blevins strikes out 18 batters (LeMoyne record) |
| 4/29/2006 | * | Canisius | 2 | at | LeMoyne | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Fairfield | 9 | at | Niagara | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Fairfield | 1 | at | Niagara | 12 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Iona | 3 | at | Siena | 11 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Iona | 0 | at | Siena | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Manhattan | 3 | at | Marist | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Manhattan | 3 | at | Marist | 4 | FINAL | Box Score | Recap | 11 innings |
| 4/29/2006 | * | St. Peter's | 3 | at | Rider | 11 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. Peter's | 1 | at | Rider | 13 | FINAL | Box Score | Recap | |
| Mid American Conference |
| 4/29/2006 | * | Buffalo | 7 | at | Akron | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Kent State | 4 | at | Ohio | 2 | FINAL | Box Score | Recap | 12 innings |
| 4/29/2006 | * | Miami, Ohio | 4 | at | Bowling Green State | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Northern Illinois | 3 | at | Eastern Michigan | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Toledo | 1 | at | Central Michigan | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Western Michigan | 5 | at | Ball State | 10 | FINAL | Box Score | Recap | |
| Mid Continent Conference |
| 4/29/2006 | * | Centenary | 17 | at | Chicago State | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Centenary | 13 | at | Chicago State | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Southern Utah | 4 | at | Oakland | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Southern Utah | 2 | at | Oakland | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Western Illinois |
| at | Oral Roberts |
| Cancelled | | Recap | CCD, rain |
| 4/29/2006 | * | Western Illinois |
| at | Oral Roberts |
| Cancelled | | Recap | CCD, rain |
| 4/29/2006 |
| North Dakota State | 1 | at | Valparaiso | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| North Dakota State | 2 | at | Valparaiso | 1 | FINAL | Box Score | Recap | |
| Mid-Eastern Athletic Conference |
| 4/29/2006 | * | Coppin State | 4 | at | Florida A&M | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Coppin State | 1 | at | Florida A&M | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Delaware State | 7 | at | North Carolina A&T | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Delaware State | 0 | at | North Carolina A&T | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Maryland-Eastern Shore | 2 | at | Bethune-Cookman | 3 | FINAL | | | Ormond Beach, FL |
| 4/29/2006 | * | Maryland-Eastern Shore | 2 | at | Bethune-Cookman | 15 | FINAL | | | Ormond Beach, FL |
| Missouri Valley Conference |
| 4/29/2006 | * | #23 Wichita State | 14 | at | Indiana State | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Illinois State | 8 | at | Evansville | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Missouri State |
| at | Bradley |
| Postponed | | Recap | PPD to 4/30, rain |
| 4/29/2006 |
| South Dakota State |
| at | Creighton |
|
| | Recap | CCD, rain |
| Mountain West Conference |
| 4/29/2006 | * | Brigham Young | 17 | at | Air Force | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Nevada-Las Vegas | 12 | at | Utah | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Texas Christian | 7 | at | San Diego State | 5 | FINAL | Box Score | Recap | 10 innings |
| 4/29/2006 |
| Cal Poly | 6 | vs | New Mexico | 4 | FINAL | Box Score | Recap | 10 innings (Corvallis, OR) |
| Northeast Conference |
| 4/29/2006 | * | Central Connecticut State | 8 | at | Fairleigh Dickinson | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Central Connecticut State | 10 | at | Fairleigh Dickinson | 0 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Monmouth | 2 | at | Sacred Heart | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Monmouth | 7 | at | Sacred Heart | 0 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Quinnipiac | 2 | at | Wagner | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Quinnipiac | 10 | at | Wagner | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. Francis | 0 | at | Mount St. Mary's | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. Francis | 1 | at | Mount St. Mary's | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Long Island | 2 | at | Columbia | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Long Island | 3 | at | Columbia | 8 | FINAL | Box Score | Recap | |
| Ohio Valley Conference |
| 4/29/2006 | * | Jacksonville State | 18 | at | Morehead State | 4 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Jacksonville State | 6 | at | Morehead State | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Murray State | 5 | at | Tennessee Tech | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Murray State | 7 | at | Tennessee Tech | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Samford | 10 | at | Eastern Kentucky | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Southeast Missouri State | 6 | at | Eastern Illinois | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Southeast Missouri State | 1 | at | Eastern Illinois | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Tennessee-Martin | 1 | at | Austin Peay State | 7 | FINAL | Box Score | | |
| 4/29/2006 | * | Tennessee-Martin | 4 | at | Austin Peay State | 7 | FINAL | Box Score | | |
| Pac 10 Conference |
| 4/29/2006 |
| Cal Poly | 4 | at | #6 Oregon State | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #16 Arizona State | 11 | at | Stanford | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Arizona | 15 | at | Washington | 0 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Southern California | 7 | at | Washington State | 13 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | UCLA | 2 | at | California | 3 | FINAL | Box Score | Recap | 11 innings |
| Patriot League |
| 4/29/2006 | * | Lafayette | 2 | at | Holy Cross | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Lafayette | 2 | at | Holy Cross | 1 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Lehigh | 1 | at | Army | 8 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Lehigh | 6 | at | Army | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Navy | 0 | at | Bucknell | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Navy | 8 | at | Bucknell | 10 | FINAL | Box Score | Recap | |
| Southeastern Conference |
| 4/29/2006 | * | Auburn | 7 | at | #8 Alabama | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #11 Arkansas | 4 | at | #29 Louisiana State | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #19 Mississippi State | 7 | at | #13 South Carolina | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | #26 Kentucky | 11 | at | #30 Vanderbilt | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Georgia | 9 | at | Florida | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Tennessee | 13 | at | Mississippi | 21 | FINAL | Box Score | Recap | |
| Southern Conference |
| 4/29/2006 | * | Davidson | 12 | at | Western Carolina | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Furman | 1 | at | North Carolina-Greensboro | 2 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Georgia Southern | 6 | at | Elon | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | The Citadel | 7 | at | Wofford | 4 | FINAL | Box Score | Recap | |
| Southland Conference |
| 4/29/2006 | * | Lamar | 9 | at | Texas State | 3 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | McNeese State |
| at | Louisiana-Monroe |
| Postponed | | Recap | PPD to 4/30, rain |
| 4/29/2006 | * | Nicholls State | 4 | at | Northwestern State | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Stephen F. Austin | 5 | at | Texas-San Antonio | 6 | FINAL | Box Score | Recap | 12 innings |
| 4/29/2006 | * | Texas-Arlington | 7 | at | Southeastern Louisiana | 9 | FINAL | Box Score | Recap | |
| Southwestern Athletic Conference |
| 4/29/2006 | * | Alabama A&M | 4 | at | Alabama State | 13 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Alabama A&M | 10 | at | Alabama State | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Alcorn State |
| at | Jackson State |
| Suspended | | Recap | suspended to 4/30, rain (4-3 JSU, Top 4) |
| 4/29/2006 | * | Grambling State | 1 | at | Texas Southern | 5 | FINAL | | | |
| 4/29/2006 | * | Grambling State | 6 | at | Texas Southern | 4 | FINAL | | | |
| 4/29/2006 | * | Southern | 0 | at | Prairie View A&M | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Arkansas-Pine Bluff |
| at | Memphis |
| Cancelled | | Recap | CCD, rain |
| 4/29/2006 |
| Arkansas-Pine Bluff |
| vs | Mississippi Valley State |
| Cancelled | | Recap | CCD, rain (Memphis, TN) |
| Sun Belt Conference |
| 4/29/2006 | * | New Orleans | 4 | at | #25 Troy | 2 | FINAL | Box Score | Recap | moved from 4/30, impending weather |
| 4/29/2006 | * | New Orleans | 5 | at | #25 Troy | 9 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Arkansas State | 4 | at | Middle Tennessee State | 7 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Louisiana-Lafayette |
| at | Arkansas-Little Rock |
| Postponed | | Recap | PPD to 4/30, rain |
| 4/29/2006 | * | South Alabama | 13 | at | Western Kentucky | 9 | FINAL | Box Score | Recap | |
| West Coast Conference |
| 4/29/2006 | * | Gonzaga | 3 | at | Loyola Marymount | 6 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | Portland | 2 | at | Pepperdine | 10 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | San Diego | 0 | at | San Francisco | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | St. Mary's | 6 | at | Santa Clara | 10 | FINAL | Box Score | Recap | |
| Western Athletic Conference |
| 4/29/2006 | * | Cal State Sacramento | 2 | at | Hawaii | 5 | FINAL | | | |
| 4/29/2006 | * | Louisiana Tech | 4 | at | New Mexico State | 5 | FINAL | Box Score | Recap | |
| 4/29/2006 | * | San Jose State | 8 | at | Nevada | 6 | FINAL | Box Score | Recap | 10 innings |
| 4/29/2006 |
| Dallas Baptist | 4 | at | Fresno State | 13 | FINAL | Box Score | Recap | |
| 4/29/2006 |
| Dallas Baptist | 3 | at | Fresno State | 6 | FINAL | Box Score | Recap | |