| Game Date | Conference | Road Team | Score |
| Home Team | Score | Status | Box Score | Recap | Commentary |
| National Collegiate Baseball Writers Poll |
| 4/3/2009 | * | #5 LSU | 8 | at | #1 Georgia | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #12 UC Irvine | 2 | at | #2 Cal State Fullerton | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #6 North Carolina | 4 | at | #3 Georgia Tech | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #4 Arizona State | 3 | at | Washington | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #19 Florida State | 14 | at | #7 Miami, Florida | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Tulane | 3 | at | #8 Rice | 11 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #9 Texas | 7 | at | #15 Oklahoma State | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #10 Oklahoma | 2 | at | Missouri | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #11 Baylor | 8 | at | Kansas | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #13 Texas A&M | 3 | at | Texas Tech | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #14 Arkansas | 6 | at | #28 South Carolina | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #16 East Carolina | 6 | at | UAB | 3 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Kentucky | 3 | at | #17 Mississippi | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Duke | 3 | at | #18 Clemson | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #20 Florida | 8 | at | Vanderbilt | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Maryland | 4 | at | #21 Virginia | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Gardner-Webb | 6 | at | #22 Coastal Carolina | 11 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #23 San Diego | 9 | at | Santa Clara | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #24 Ohio State | 5 | at | Minnesota | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Cal State Northridge | 10 | at | #25 Cal Poly | 11 | FINAL | Box Score | Recap | 10 innings |
| 4/3/2009 | * | Gonzaga | 3 | at | #26 Pepperdine | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | New Mexico | 3 | at | #27 TCU | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| UC Davis | 0 | at | #29 San Diego State | 14 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #30 UNC Wilmington | 2 | at | George Mason | 4 | FINAL | Box Score | Recap | |
| America East Conference |
| 4/3/2009 |
| Iona | 3 | at | Maine | 17 | FINAL | Box Score | Recap | 7 innings |
| Atlantic 10 Conference |
| 4/3/2009 | * | Charlotte |
| at | Duquesne |
| Postponed | | Recap | PPD to 4/4, inclement weather |
| 4/3/2009 | * | Dayton |
| at | Rhode Island |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 | * | George Washington |
| at | St. Bonaventure |
| Canceled | | Recap | CCD, inclement weather |
| 4/3/2009 | * | Richmond | 6 | at | St. Louis | 13 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | St. Joseph's |
| at | Fordham |
| Postponed | | Recap | PPD to 4/4, rain |
| 4/3/2009 | * | Temple |
| at | Massachusetts |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 | * | Xavier |
| at | LaSalle |
| Postponed | | Recap | PPD to 4/4, rain |
| Atlantic Coast Conference |
| 4/3/2009 | * | #6 North Carolina | 4 | at | #3 Georgia Tech | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #19 Florida State | 14 | at | #7 Miami, Florida | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Duke | 3 | at | #18 Clemson | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Maryland | 4 | at | #21 Virginia | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | NC State |
| at | Boston College |
| Postponed | | Recap | PPD to 4/4, rain |
| 4/3/2009 | * | Wake Forest | 11 | at | Virginia Tech | 4 | FINAL | Box Score | Recap | |
| Atlantic Sun Conference |
| 4/3/2009 | * | Florida Gulf Coast | 7 | at | Mercer | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Jacksonville | 3 | at | Belmont | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Lipscomb | 1 | at | Kennesaw State | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Stetson | 12 | at | South Carolina-Upstate | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Savannah State |
| at | Campbell |
| Canceled | | Recap | CCD |
| Big 10 Conference |
| 4/3/2009 | * | #24 Ohio State | 5 | at | Minnesota | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Indiana | 14 | at | Illinois | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Iowa | 15 | at | Purdue | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Northwestern |
| at | Michigan State |
| Postponed | | Recap | PPD to 4/4, impending weather |
| Big 12 Conference |
| 4/3/2009 | * | #9 Texas | 7 | at | #15 Oklahoma State | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #10 Oklahoma | 2 | at | Missouri | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #11 Baylor | 8 | at | Kansas | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #13 Texas A&M | 3 | at | Texas Tech | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Kansas State | 15 | at | Nebraska | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Kansas State | 9 | at | Nebraska | 3 | FINAL | Box Score | Recap | moved from 4/5, impending weather |
| Big East Conference |
| 4/3/2009 | * | Connecticut | 7 | at | Seton Hall | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Georgetown |
| at | West Virginia |
| Postponed | | Recap | PPD to 4/4, inclement weather |
| 4/3/2009 | * | Louisville | 13 | at | Cincinnati | 3 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Pittsburgh | 1 | at | South Florida | 8 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Rutgers |
| at | St. John's |
| Postponed | | Recap | PPD to 4/4, inclement weather |
| 4/3/2009 | * | Villanova | 1 | at | Notre Dame | 3 | FINAL | Box Score | Recap | |
| Big South Conference |
| 4/3/2009 | * | Gardner-Webb | 6 | at | #22 Coastal Carolina | 11 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Charleston Southern | 4 | at | Winthrop | 10 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Liberty | 6 | at | VMI | 13 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Presbyterian | 5 | at | High Point | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Radford | 8 | at | UNC Asheville | 4 | FINAL | Box Score | Recap | |
| Big West Conference |
| 4/3/2009 | * | #12 UC Irvine | 2 | at | #2 Cal State Fullerton | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Cal State Northridge | 10 | at | #25 Cal Poly | 11 | FINAL | Box Score | Recap | 10 innings |
| 4/3/2009 |
| UC Davis | 0 | at | #29 San Diego State | 14 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Pacific | 8 | at | UC Santa Barbara | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | UC Riverside | 2 | at | Long Beach State | 5 | FINAL | Box Score | Recap | |
| Colonial Athletic Association |
| 4/3/2009 | * | #30 UNC Wilmington | 2 | at | George Mason | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Georgia State |
| at | Delaware |
| Postponed | | Recap | PPD to 4/4, inclement weather |
| 4/3/2009 | * | Hofstra | 8 | at | VCU | 10 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Old Dominion | 3 | at | James Madison | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | William and Mary |
| at | Northeastern |
| Postponed | | Recap | PPD to 4/4, rain |
| Conference USA |
| 4/3/2009 | * | Tulane | 3 | at | #8 Rice | 11 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #16 East Carolina | 6 | at | UAB | 3 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Marshall | 2 | at | Southern Mississippi | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | UCF | 5 | at | Memphis | 10 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| UT Pan American | 2 | at | Houston | 15 | FINAL | Box Score | Recap | |
| Division I Independents |
| 4/3/2009 |
| Air Force | 7 | at | Utah Valley State | 13 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 |
| Air Force | 10 | at | Utah Valley State | 12 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Cal State Bakersfield | 8 | at | Fresno State | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Houston Baptist | 2 | at | Dallas Baptist | 12 | FINAL | Box Score | Recap | 8 innings, run rule |
| 4/3/2009 |
| LeMoyne |
| at | Wright State |
| Postponed | | Recap | PPD to 4/4, rain |
| 4/3/2009 |
| North Carolina Central | 2 | at | Florida A&M | 3 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 |
| North Carolina Central | 1 | at | Florida A&M | 17 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 |
| North Dakota | 7 | at | Bradley | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Savannah State |
| at | Campbell |
| Canceled | | Recap | CCD |
| 4/3/2009 |
| Southern Illinois-Edwardsville | 5 | at | Austin Peay State | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Urbana |
| at | Chicago State |
| Postponed | | Recap | PPD to 4/5, field conditions |
| 4/3/2009 |
| UT Pan American | 2 | at | Houston | 15 | FINAL | Box Score | Recap | |
| Horizon League |
| 4/3/2009 | * | Butler |
| at | Youngstown State |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 | * | Illinois-Chicago | 3 | at | Wisconsin-Milwaukee | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Valparaiso |
| at | Cleveland State |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 |
| LeMoyne |
| at | Wright State |
| Postponed | | Recap | PPD to 4/4, rain |
| Metro Atlantic Athletic Conference |
| 4/3/2009 |
| Iona | 3 | at | Maine | 17 | FINAL | Box Score | Recap | 7 innings |
| Mid American Conference |
| 4/3/2009 | * | Akron | 4 | at | Eastern Michigan | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Ball State |
| at | Buffalo |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 | * | Bowling Green State | 14 | at | Central Michigan | 10 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Miami, Ohio | 9 | at | Western Michigan | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Northern Illinois | 3 | at | Kent State | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Toledo |
| at | Ohio |
| Postponed | | Recap | PPD to 4/4, inclement weather |
| Mid-Eastern Athletic Conference |
| 4/3/2009 |
| North Carolina Central | 2 | at | Florida A&M | 3 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 |
| North Carolina Central | 1 | at | Florida A&M | 17 | FINAL | Box Score | Recap | 7 innings |
| Missouri Valley Conference |
| 4/3/2009 | * | Creighton | 7 | at | Evansville | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Illinois State | 5 | at | Wichita State | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Indiana State | 9 | at | Northern Iowa | 3 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Missouri State | 10 | at | Southern Illinois | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| North Dakota | 7 | at | Bradley | 4 | FINAL | Box Score | Recap | |
| Mountain West Conference |
| 4/3/2009 | * | New Mexico | 3 | at | #27 TCU | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| UC Davis | 0 | at | #29 San Diego State | 14 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Utah | 8 | at | UNLV | 5 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Air Force | 7 | at | Utah Valley State | 13 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 |
| Air Force | 10 | at | Utah Valley State | 12 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| BYU | 15 | at | Western Carolina | 11 | FINAL | Box Score | Recap | |
| Northeast Conference |
| 4/3/2009 | * | Central Connecticut State | 1 | at | Wagner | 10 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Fairleigh Dickinson |
| at | Sacred Heart |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 | * | Long Island |
| at | Monmouth |
| Postponed | | Recap | PPD to 4/5, rain |
| 4/3/2009 | * | Quinnipiac |
| at | Mount St. Mary's |
| Postponed | | Recap | PPD to 4/5, rain |
| Ohio Valley Conference |
| 4/3/2009 |
| Southern Illinois-Edwardsville | 5 | at | Austin Peay State | 7 | FINAL | Box Score | Recap | |
| Pac 10 Conference |
| 4/3/2009 | * | #4 Arizona State | 3 | at | Washington | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | California | 4 | at | Oregon State | 8 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Southern California | 6 | at | Arizona | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Stanford | 1 | at | Oregon | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | UCLA | 2 | at | Washington State | 7 | FINAL | Box Score | Recap | |
| Southeastern Conference |
| 4/3/2009 | * | #5 LSU | 8 | at | #1 Georgia | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #14 Arkansas | 6 | at | #28 South Carolina | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Kentucky | 3 | at | #17 Mississippi | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | #20 Florida | 8 | at | Vanderbilt | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Auburn | 9 | at | Mississippi State | 8 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Tennessee | 2 | at | Alabama | 9 | FINAL | Box Score | Recap | |
| Southern Conference |
| 4/3/2009 | * | Appalachian State | 3 | at | Furman | 5 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | College of Charleston | 14 | at | Georgia Southern | 15 | FINAL | Box Score | Recap | 14 innings |
| 4/3/2009 | * | Davidson | 4 | at | Samford | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | UNC Greensboro | 1 | at | Elon | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Wofford | 3 | at | The Citadel | 13 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| BYU | 15 | at | Western Carolina | 11 | FINAL | Box Score | Recap | |
| Southland Conference |
| 4/3/2009 | * | Nicholls State | 2 | at | Northwestern State | 5 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Sam Houston State | 7 | at | McNeese State | 5 | FINAL | Box Score | Recap | 10 innings |
| 4/3/2009 | * | Southeastern Louisiana | 8 | at | UT Arlington | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Texas A&M-Corpus Christi | 1 | at | Lamar | 3 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Texas State | 5 | at | Central Arkansas | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | UTSA | 12 | at | Stephen F. Austin | 8 | FINAL | Box Score | Recap | |
| Southwestern Athletic Conference |
| 4/3/2009 | * | Alcorn State | 1 | at | Jackson State | 3 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 | * | Alcorn State | 7 | at | Jackson State | 5 | FINAL | Box Score | Recap | 7 innings |
| 4/3/2009 |
| Grambling State | 11 | at | New Orleans | 14 | FINAL | Box Score | Recap | |
| Summit League |
| 4/3/2009 | * | IUPU-Fort Wayne | 0 | at | Oral Roberts | 19 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | North Dakota State |
| at | Southern Utah |
| Canceled | | Recap | CCD, rain (St. George, UT (moved from Cedar City, snow)) |
| 4/3/2009 | * | North Dakota State |
| at | Southern Utah |
| Postponed | | Recap | PPD to 4/4, inclement weather |
| 4/3/2009 | * | South Dakota State | 1 | at | Centenary | 10 | FINAL | Box Score | Recap | |
| Sun Belt Conference |
| 4/3/2009 | * | Louisiana-Monroe | 24 | at | Arkansas-Little Rock | 5 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Middle Tennessee State | 2 | at | Louisiana-Lafayette | 5 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | South Alabama | 5 | at | Florida Atlantic | 6 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Troy | 5 | at | Arkansas State | 2 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Western Kentucky | 8 | at | Florida International | 9 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Grambling State | 11 | at | New Orleans | 14 | FINAL | Box Score | Recap | |
| West Coast Conference |
| 4/3/2009 | * | #23 San Diego | 9 | at | Santa Clara | 4 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Gonzaga | 3 | at | #26 Pepperdine | 1 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Portland | 6 | at | Loyola Marymount | 11 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | St. Mary's | 5 | at | San Francisco | 2 | FINAL | Box Score | Recap | |
| Western Athletic Conference |
| 4/3/2009 | * | Nevada | 8 | at | Louisiana Tech | 5 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | Sacramento State | 6 | at | New Mexico State | 7 | FINAL | Box Score | Recap | |
| 4/3/2009 | * | San Jose State | 0 | at | Hawaii | 3 | FINAL | Box Score | Recap | |
| 4/3/2009 |
| Cal State Bakersfield | 8 | at | Fresno State | 9 | FINAL | Box Score | Recap | |