| Game Date | Conference | Road Team | Score |
| Home Team | Score | Status | Box Score | Recap | Commentary |
| National Collegiate Baseball Writers Poll |
| 5/5/2006 | * | #4 Cal State Fullerton | 5 | at | UC Santa Barbara | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Washington | 6 | at | #6 Oregon State | 4 | FINAL | Box Score | Recap | Tim Lincecum (UW) sets Pac-10 career mark with 460 Ks |
| 5/5/2006 | * | #7 Alabama | 3 | at | #15 Arkansas | 4 | FINAL | Box Score | Recap | Alabama issues school record 16 walks (11 innings) |
| 5/5/2006 | * | Kansas | 4 | at | #8 Texas | 7 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Kansas State |
| at | #9 Oklahoma |
| Postponed | | Recap | PPD to 5/6, rain |
| 5/5/2006 |
| South Florida | 3 | at | #10 Georgia Tech | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #12 South Carolina | 4 | at | Georgia | 8 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #13 Florida State | 2 | at | #29 Wake Forest | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Louisville | 3 | at | #14 Notre Dame | 11 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | UCF | 5 | at | #16 Houston | 10 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Marshall | 0 | at | #17 Tulane | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #26 Mississippi | 3 | at | #19 Kentucky | 8 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Virginia Commonwealth | 0 | at | #21 Old Dominion | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #23 Wichita State | 3 | at | Illinois State | 5 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Wright State | 2 | at | #24 Miami, Florida | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #25 Winthrop | 23 | at | Charleston Southern | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Florida | 2 | at | #27 Mississippi State | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #28 Louisiana State | 4 | at | Auburn | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #30 Troy | 7 | at | Louisiana-Lafayette | 15 | FINAL | Box Score | Recap | |
| America East Conference |
| 5/5/2006 | * | Albany | 10 | at | Maine | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Binghamton | 14 | at | Hartford | 0 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Stony Brook | 2 | at | Vermont | 3 | FINAL | Box Score | Recap | |
| Atlantic 10 Conference |
| 5/5/2006 | * | Duquesne | 6 | at | St. Joseph's | 5 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Fordham | 11 | at | Rhode Island | 2 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | North Carolina-Charlotte | 5 | at | Dayton | 6 | FINAL | Box Score | Recap | 11 innings |
| 5/5/2006 | * | Richmond | 2 | at | LaSalle | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | St. Bonaventure | 7 | at | Massachusetts | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | St. Louis | 7 | at | George Washington | 5 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Temple | 4 | at | Xavier | 5 | FINAL | Box Score | Recap | 10 innings |
| Atlantic Coast Conference |
| 5/5/2006 |
| South Florida | 3 | at | #10 Georgia Tech | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #13 Florida State | 2 | at | #29 Wake Forest | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Wright State | 2 | at | #24 Miami, Florida | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Maryland | 11 | at | Boston College | 10 | FINAL | Box Score | Recap | |
| Atlantic Sun Conference |
| 5/5/2006 | * | Lipscomb | 6 | at | Florida Atlantic | 10 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Stetson | 10 | at | East Tennessee State | 11 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Campbell |
| at | North Carolina-Asheville |
| Postponed | | Recap | PPD to 5/6, rain |
| Big 10 Conference |
| 5/5/2006 | * | Iowa | 3 | at | Indiana | 2 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Michigan | 1 | at | Illinois | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Minnesota | 15 | at | Northwestern | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Ohio State | 16 | at | Michigan State | 2 | FINAL | Box Score | Recap | |
| Big 12 Conference |
| 5/5/2006 | * | Kansas | 4 | at | #8 Texas | 7 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Kansas State |
| at | #9 Oklahoma |
| Postponed | | Recap | PPD to 5/6, rain |
| 5/5/2006 |
| Dallas Baptist | 6 | at | Texas A&M | 1 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Mississippi Valley State | 1 | at | Missouri | 12 | FINAL | Box Score | Recap | |
| Big East Conference |
| 5/5/2006 |
| South Florida | 3 | at | #10 Georgia Tech | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Louisville | 3 | at | #14 Notre Dame | 11 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Cincinnati | 6 | at | Villanova | 7 | FINAL | Box Score | Recap | 11 innings |
| Big South Conference |
| 5/5/2006 | * | #25 Winthrop | 23 | at | Charleston Southern | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Campbell |
| at | North Carolina-Asheville |
| Postponed | | Recap | PPD to 5/6, rain |
| Big West Conference |
| 5/5/2006 | * | #4 Cal State Fullerton | 5 | at | UC Santa Barbara | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Long Beach State | 2 | at | Cal Poly | 8 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | UC Riverside | 11 | at | Pacific | 2 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| UC Davis | 12 | at | Cal State Northridge | 1 | FINAL | Box Score | Recap | |
| Colonial Athletic Association |
| 5/5/2006 | * | Virginia Commonwealth | 0 | at | #21 Old Dominion | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Delaware | 3 | at | North Carolina-Wilmington | 4 | FINAL | Box Score | Recap | 11 innings |
| 5/5/2006 | * | George Mason | 17 | at | Georgia State | 14 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Hofstra | 3 | at | Northeastern | 2 | FINAL | Box Score | Recap | |
| Conference USA |
| 5/5/2006 | * | UCF | 5 | at | #16 Houston | 10 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Marshall | 0 | at | #17 Tulane | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Alabama-Birmingham | 4 | at | Memphis | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | East Carolina | 10 | at | Southern Mississippi | 11 | FINAL | Box Score | Recap | 11 innings |
| Division I Independents |
| 5/5/2006 |
| Dallas Baptist | 6 | at | Texas A&M | 1 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| New York Tech | 4 | at | Army | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| South Dakota State | 9 | at | North Dakota State | 5 | FINAL | Box Score | Recap | |
| Horizon League |
| 5/5/2006 |
| Wright State | 2 | at | #24 Miami, Florida | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Illinois-Chicago | 7 | at | Youngstown State | 2 | FINAL | Box Score | Recap | |
| Mid American Conference |
| 5/5/2006 | * | Akron | 14 | at | Ohio | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Buffalo | 1 | at | Miami, Ohio | 2 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Buffalo | 3 | at | Miami, Ohio | 12 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Eastern Michigan | 10 | at | Central Michigan | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Kent State | 11 | at | Bowling Green State | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Northern Illinois | 4 | at | Western Michigan | 7 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Toledo | 6 | at | Ball State | 14 | FINAL | Box Score | Recap | |
| Missouri Valley Conference |
| 5/5/2006 | * | #23 Wichita State | 3 | at | Illinois State | 5 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Creighton | 10 | at | Missouri State | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Indiana State | 1 | at | Southern Illinois | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Northern Iowa | 2 | at | Bradley | 6 | FINAL | Box Score | Recap | |
| Mountain West Conference |
| 5/5/2006 | * | New Mexico | 6 | at | Brigham Young | 10 | FINAL | Box Score | Recap | makeup of 5/4 game |
| 5/5/2006 | * | New Mexico | 2 | at | Brigham Young | 9 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | San Diego State | 36 | at | Air Force | 11 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Utah | 0 | at | Texas Christian | 2 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Nevada-Las Vegas | 6 | at | Arizona | 7 | FINAL | Box Score | Recap | 11 innings |
| Pac 10 Conference |
| 5/5/2006 | * | Washington | 6 | at | #6 Oregon State | 4 | FINAL | Box Score | Recap | Tim Lincecum (UW) sets Pac-10 career mark with 460 Ks |
| 5/5/2006 | * | California | 2 | at | Stanford | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 |
| Nevada-Las Vegas | 6 | at | Arizona | 7 | FINAL | Box Score | Recap | 11 innings |
| Patriot League |
| 5/5/2006 |
| New York Tech | 4 | at | Army | 9 | FINAL | Box Score | Recap | |
| Southeastern Conference |
| 5/5/2006 | * | #7 Alabama | 3 | at | #15 Arkansas | 4 | FINAL | Box Score | Recap | Alabama issues school record 16 walks (11 innings) |
| 5/5/2006 | * | #12 South Carolina | 4 | at | Georgia | 8 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #26 Mississippi | 3 | at | #19 Kentucky | 8 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Florida | 2 | at | #27 Mississippi State | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | #28 Louisiana State | 4 | at | Auburn | 3 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Vanderbilt | 3 | at | Tennessee | 13 | FINAL | Box Score | Recap | |
| Southern Conference |
| 5/5/2006 | * | Appalachian State | 2 | at | The Citadel | 7 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Elon | 15 | at | Furman | 7 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | North Carolina-Greensboro | 3 | at | Western Carolina | 8 | FINAL | Box Score | Recap | |
| Southland Conference |
| 5/5/2006 | * | Sam Houston State | 9 | at | Texas-Arlington | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Southeastern Louisiana |
| at | McNeese State |
| Postponed | | Recap | PPD to 5/6, rain |
| 5/5/2006 | * | Texas-San Antonio | 3 | at | Louisiana-Monroe | 5 | FINAL | Box Score | Recap | |
| Southwestern Athletic Conference |
| 5/5/2006 |
| Mississippi Valley State | 1 | at | Missouri | 12 | FINAL | Box Score | Recap | |
| Sun Belt Conference |
| 5/5/2006 | * | #30 Troy | 7 | at | Louisiana-Lafayette | 15 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Middle Tennessee State | 10 | at | Florida International | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | South Alabama | 12 | at | New Orleans | 10 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Western Kentucky | 4 | at | Arkansas State | 21 | FINAL | Box Score | Recap | |
| West Coast Conference |
| 5/5/2006 | * | Pepperdine | 1 | at | Gonzaga | 6 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | San Francisco | 6 | at | St. Mary's | 4 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Santa Clara | 6 | at | San Diego | 7 | FINAL | Box Score | Recap | |
| Western Athletic Conference |
| 5/5/2006 | * | Hawaii | 9 | at | Louisiana Tech | 2 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | Nevada | 2 | at | Fresno State | 13 | FINAL | Box Score | Recap | |
| 5/5/2006 | * | New Mexico State | 6 | at | San Jose State | 7 | FINAL | Box Score | Recap | 10 innings |