| Game Date | Conference | Road Team | Score |
| Home Team | Score | Status | Box Score | Recap | Commentary |
| National Collegiate Baseball Writers Poll |
| 5/3/2009 | * | #2 Arizona State | 5 | at | #29 Oregon State | 10 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #3 Rice | 6 | at | Houston | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Cal State Northridge | 2 | at | #4 UC Irvine | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #5 LSU | 4 | at | #12 Arkansas | 3 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | UC Santa Barbara | 3 | at | #6 Cal State Fullerton | 15 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #20 Florida | 10 | at | #7 Georgia | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #8 Mississippi | 11 | at | Auburn | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Virginia Tech | 4 | at | #9 Florida State | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #10 Texas | 3 | at | #24 Baylor | 1 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Kansas | 9 | at | #11 Oklahoma | 10 | FINAL | Box Score | Recap | 10 innings (makeup of 5/2 game) |
| 5/3/2009 | * | #13 Miami, Florida | 3 | at | Boston College | 13 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Presbyterian | 3 | at | #14 Georgia Tech | 23 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| San Francisco | 4 | at | #16 Cal Poly | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Maryland | 4 | at | #19 Clemson | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Maryland | 8 | at | #19 Clemson | 6 | FINAL | Box Score | Recap | moved from 5/4, impending weather |
| 5/3/2009 |
| Louisiana-Lafayette | 4 | at | #21 East Carolina | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Liberty | 2 | at | #22 Coastal Carolina | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #23 Kansas State |
| at | #26 Oklahoma State |
| Canceled | | Recap | CCD, rain and field conditions (makeup of 5/2 game) |
| 5/3/2009 | * | Michigan | 9 | at | #25 Ohio State | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #27 Alabama | 17 | at | Mississippi State | 16 | FINAL | Box Score | Recap | Resumption of 5/2 game |
| 5/3/2009 | * | #27 Alabama |
| at | Mississippi State |
| Canceled | | Recap | CCD, inclement weather |
| 5/3/2009 | * | #30 San Diego | 4 | at | Loyola Marymount | 5 | FINAL | Box Score | Recap | |
| America East Conference |
| 5/3/2009 | * | Binghamton |
| at | UMBC |
| Postponed | | Recap | PPD, rain |
| 5/3/2009 | * | Binghamton |
| at | UMBC |
| Postponed | | Recap | PPD, rain |
| 5/3/2009 | * | Hartford | 7 | at | Vermont | 10 | FINAL | Box Score | Recap | 7 innings |
| 5/3/2009 | * | Hartford | 5 | at | Vermont | 14 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Stony Brook |
| at | Rider |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 |
| Stony Brook |
| at | Rider |
| Canceled | | Recap | CCD, rain |
| Atlantic 10 Conference |
| 5/3/2009 | * | Dayton | 13 | at | Duquesne | 10 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Fordham | 6 | at | Rhode Island | 7 | FINAL | Box Score | Recap | 12 innings |
| 5/3/2009 | * | LaSalle | 8 | at | Charlotte | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | St. Bonaventure | 7 | at | Massachusetts | 12 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Temple | 6 | at | Richmond | 8 | FINAL | Box Score | Recap | |
| Atlantic Coast Conference |
| 5/3/2009 | * | Virginia Tech | 4 | at | #9 Florida State | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #13 Miami, Florida | 3 | at | Boston College | 13 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Presbyterian | 3 | at | #14 Georgia Tech | 23 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Maryland | 4 | at | #19 Clemson | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Maryland | 8 | at | #19 Clemson | 6 | FINAL | Box Score | Recap | moved from 5/4, impending weather |
| 5/3/2009 |
| North Carolina Central | 2 | at | NC State | 15 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| North Carolina Central | 5 | at | NC State | 15 | FINAL | Box Score | Recap | |
| Atlantic Sun Conference |
| 5/3/2009 | * | Belmont | 8 | at | Lipscomb | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Jacksonville | 9 | at | Kennesaw State | 15 | FINAL | Box Score | Recap | makeup of 5/2 game |
| 5/3/2009 | * | North Florida | 8 | at | Stetson | 10 | FINAL | Box Score | Recap | |
| Big 10 Conference |
| 5/3/2009 | * | Michigan | 9 | at | #25 Ohio State | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Illinois | 9 | at | Northwestern | 0 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Indiana | 2 | at | Purdue | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Iowa | 3 | at | Minnesota | 12 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Penn State | 5 | at | Michigan State | 6 | FINAL | Box Score | Recap | |
| Big 12 Conference |
| 5/3/2009 | * | #10 Texas | 3 | at | #24 Baylor | 1 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Kansas | 9 | at | #11 Oklahoma | 10 | FINAL | Box Score | Recap | 10 innings (makeup of 5/2 game) |
| 5/3/2009 | * | #23 Kansas State |
| at | #26 Oklahoma State |
| Canceled | | Recap | CCD, rain and field conditions (makeup of 5/2 game) |
| 5/3/2009 | * | Missouri | 12 | at | Nebraska | 9 | FINAL | Box Score | Recap | |
| Big East Conference |
| 5/3/2009 | * | Cincinnati | 5 | at | South Florida | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Connecticut | 4 | at | Notre Dame | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Louisville |
| at | Villanova |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 | * | Pittsburgh |
| at | Georgetown |
| Canceled | | Recap | CCD, inclement weather |
| 5/3/2009 | * | Rutgers | 3 | at | West Virginia | 9 | FINAL | Box Score | Recap | |
| Big South Conference |
| 5/3/2009 |
| Presbyterian | 3 | at | #14 Georgia Tech | 23 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Liberty | 2 | at | #22 Coastal Carolina | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | UNC Asheville | 0 | at | Winthrop | 15 | FINAL | Box Score | Recap | |
| Big West Conference |
| 5/3/2009 | * | Cal State Northridge | 2 | at | #4 UC Irvine | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | UC Santa Barbara | 3 | at | #6 Cal State Fullerton | 15 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| San Francisco | 4 | at | #16 Cal Poly | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Pacific | 1 | at | UC Riverside | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | UC Davis | 2 | at | Long Beach State | 3 | FINAL | Box Score | Recap | |
| Colonial Athletic Association |
| 5/3/2009 | * | Delaware |
| at | UNC Wilmington |
| Canceled | | Recap | CCD, health concerns |
| 5/3/2009 | * | James Madison |
| at | William and Mary |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 | * | Towson | 17 | at | Hofstra | 1 | FINAL | Box Score | Recap | 7 innings, rain |
| 5/3/2009 | * | VCU | 4 | at | Georgia State | 5 | FINAL | Box Score | Recap | |
| Conference USA |
| 5/3/2009 | * | #3 Rice | 6 | at | Houston | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Louisiana-Lafayette | 4 | at | #21 East Carolina | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Marshall | 7 | at | UCF | 8 | FINAL | Box Score | Recap | 11 innings |
| 5/3/2009 | * | Memphis |
| at | UAB |
| Canceled | | Recap | CCD, weather and field conditions |
| 5/3/2009 | * | Tulane | 8 | at | Southern Mississippi | 4 | FINAL | Box Score | Recap | 5 innings, rain and lightning |
| Division I Independents |
| 5/3/2009 |
| Houston Baptist | 1 | at | New Mexico State | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Lafayette | 3 | at | LeMoyne | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Longwood | 7 | at | UMES | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Longwood | 15 | at | UMES | 2 | FINAL | Box Score | Recap | 7 innings |
| 5/3/2009 |
| New Jersey Tech | 0 | at | Army | 17 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| New York Tech |
| at | Navy |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 |
| New York Tech |
| at | Navy |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 |
| North Carolina Central | 2 | at | NC State | 15 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| North Carolina Central | 5 | at | NC State | 15 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Southern Illinois-Edwardsville | 10 | at | Evansville | 9 | FINAL | Box Score | Recap | 13 innings |
| 5/3/2009 |
| Utah Valley State | 23 | at | Northern Colorado | 21 | FINAL | Box Score | Recap | |
| Horizon League |
| 5/3/2009 | * | Cleveland State | 5 | vs | Wisconsin-Milwaukee | 3 | FINAL | Box Score | Recap | makeup of 4/26 game (Lorain, OH) |
| 5/3/2009 | * | Wisconsin-Milwaukee | 12 | at | Cleveland State | 1 | FINAL | Box Score | Recap | |
| Ivy League |
| 5/3/2009 | IVY-03 | Cornell | 0 | vs | Dartmouth | 10 | FINAL | Box Score | Recap | Ivy League Championship, Game 3 (Hanover, NH) |
| Metro Atlantic Athletic Conference |
| 5/3/2009 | * | Canisius | 7 | at | Siena | 1 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Iona | 0 | at | Fairfield | 12 | FINAL | Box Score | Recap | 5 innings, rain |
| 5/3/2009 | * | Manhattan | 8 | at | Niagara | 10 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Marist | 4 | at | St. Peter's | 7 | FINAL | Box Score | Recap | 8 innings, rain |
| 5/3/2009 |
| Stony Brook |
| at | Rider |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 |
| Stony Brook |
| at | Rider |
| Canceled | | Recap | CCD, rain |
| Mid American Conference |
| 5/3/2009 | * | Ball State | 13 | at | Eastern Michigan | 14 | FINAL | Box Score | Recap | 10 innings |
| 5/3/2009 | * | Kent State | 16 | at | Buffalo | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Miami, Ohio | 2 | at | Akron | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Northern Illinois | 4 | at | Central Michigan | 22 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Ohio | 7 | at | Bowling Green State | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Western Michigan | 16 | at | Toledo | 5 | FINAL | Box Score | Recap | |
| Mid-Eastern Athletic Conference |
| 5/3/2009 | * | Coppin State | 9 | at | North Carolina A&T | 14 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Delaware State | 1 | at | Bethune-Cookman | 11 | FINAL | Box Score | Recap | 7 innings |
| 5/3/2009 | * | Norfolk State | 13 | at | Florida A&M | 2 | FINAL | Box Score | Recap | 7 innings |
| 5/3/2009 |
| Longwood | 7 | at | UMES | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| Longwood | 15 | at | UMES | 2 | FINAL | Box Score | Recap | 7 innings |
| Missouri Valley Conference |
| 5/3/2009 | * | Creighton | 10 | at | Illinois State | 6 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Indiana State | 5 | at | Wichita State | 3 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Northern Iowa |
| at | Missouri State |
| Canceled | | Recap | CCD, rain (makeup of 5/1 game) |
| 5/3/2009 | * | Southern Illinois | 11 | at | Bradley | 1 | FINAL | Box Score | Recap | 8 innings, run rule |
| 5/3/2009 |
| Southern Illinois-Edwardsville | 10 | at | Evansville | 9 | FINAL | Box Score | Recap | 13 innings |
| Mountain West Conference |
| 5/3/2009 | * | UNLV | 13 | at | New Mexico | 11 | FINAL | Box Score | Recap | 10 innings |
| 5/3/2009 | * | Utah | 12 | at | Air Force | 6 | FINAL | Box Score | Recap | makeup of 5/2 game |
| 5/3/2009 | * | Utah | 19 | at | Air Force | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| San Diego State | 4 | at | Santa Clara | 3 | FINAL | Box Score | Recap | |
| Northeast Conference |
| 5/3/2009 | * | Fairleigh Dickinson | 8 | at | Central Connecticut State | 14 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Monmouth |
| at | Mount St. Mary's |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 | * | Monmouth |
| at | Mount St. Mary's |
| Canceled | | Recap | CCD, rain (makeup of 5/1 game) |
| 5/3/2009 | * | Sacred Heart | 3 | at | Quinnipiac | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Wagner |
| at | Long Island |
| Canceled | | Recap | CCD, rain |
| Ohio Valley Conference |
| 5/3/2009 | * | Austin Peay State | 1 | at | Tennessee-Martin | 6 | FINAL | Box Score | Recap | 5 innings, rain |
| 5/3/2009 | * | Eastern Illinois |
| at | Southeast Missouri State |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 | * | Morehead State |
| at | Jacksonville State |
| Canceled | | Recap | CCD, inclement weather |
| 5/3/2009 | * | Tennessee Tech | 1 | at | Murray State | 1 | FINAL | Box Score | Recap | 5 innings, rain |
| Pac 10 Conference |
| 5/3/2009 | * | #2 Arizona State | 5 | at | #29 Oregon State | 10 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | California | 8 | at | Arizona | 12 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Southern California | 2 | at | Washington | 3 | FINAL | Box Score | Recap | 10 innings |
| 5/3/2009 | * | Stanford | 3 | at | Washington State | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | UCLA | 8 | at | Oregon | 1 | FINAL | Box Score | Recap | |
| Patriot League |
| 5/3/2009 |
| Lafayette | 3 | at | LeMoyne | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| New Jersey Tech | 0 | at | Army | 17 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| New York Tech |
| at | Navy |
| Canceled | | Recap | CCD, rain |
| 5/3/2009 |
| New York Tech |
| at | Navy |
| Canceled | | Recap | CCD, rain |
| Southeastern Conference |
| 5/3/2009 | * | #5 LSU | 4 | at | #12 Arkansas | 3 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #20 Florida | 10 | at | #7 Georgia | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #8 Mississippi | 11 | at | Auburn | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #27 Alabama | 17 | at | Mississippi State | 16 | FINAL | Box Score | Recap | Resumption of 5/2 game |
| 5/3/2009 | * | #27 Alabama |
| at | Mississippi State |
| Canceled | | Recap | CCD, inclement weather |
| 5/3/2009 | * | Tennessee | 11 | at | Kentucky | 17 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Vanderbilt | 3 | at | South Carolina | 11 | FINAL | Box Score | Recap | |
| Southern Conference |
| 5/3/2009 | * | Davidson | 10 | at | College of Charleston | 27 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Furman | 12 | at | Georgia Southern | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Samford | 5 | at | The Citadel | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Western Carolina | 9 | at | UNC Greensboro | 4 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Wofford | 7 | at | Elon | 23 | FINAL | Box Score | Recap | |
| Southland Conference |
| 5/3/2009 | * | Lamar | 13 | at | McNeese State | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Nicholls State | 1 | at | Southeastern Louisiana | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Texas A&M-Corpus Christi | 4 | at | UT Arlington | 14 | FINAL | Box Score | Recap | 7 innings, run rule |
| 5/3/2009 | * | Texas State | 5 | at | UTSA | 3 | FINAL | Box Score | Recap | 11 innings |
| Southwestern Athletic Conference |
| 5/3/2009 | * | Alcorn State |
| at | Mississippi Valley State |
| Postponed | | | PPD, rain |
| 5/3/2009 | * | Alcorn State |
| at | Mississippi Valley State |
| Postponed | | | PPD, rain (makeup of 5/2 game) |
| 5/3/2009 | * | Jackson State |
| at | Alabama State |
| Suspended | | Recap | Suspended, inclement weather (5-1 JSU) |
| 5/3/2009 | * | Prairie View A&M | 11 | at | Texas Southern | 10 | FINAL | Box Score | | |
| 5/3/2009 | * | Southern |
| at | Grambling State |
| Postponed | | | PPD, inclement weather |
| Summit League |
| 5/3/2009 | * | Centenary | 11 | at | North Dakota State | 2 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Oakland | 5 | at | South Dakota State | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Southern Utah |
| at | Oral Roberts |
| Canceled | | Recap | CCD, field conditions |
| 5/3/2009 | * | Southern Utah |
| at | Oral Roberts |
| Canceled | | Recap | CCD, field conditions (makeup of 5/1 game) |
| 5/3/2009 | * | Western Illinois | 10 | at | IUPU-Fort Wayne | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Western Illinois | 0 | at | IUPU-Fort Wayne | 2 | FINAL | Box Score | Recap | 7 innings |
| Sun Belt Conference |
| 5/3/2009 |
| Louisiana-Lafayette | 4 | at | #21 East Carolina | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Arkansas State | 4 | at | Florida International | 10 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Arkansas-Little Rock | 2 | at | Western Kentucky | 12 | FINAL | Box Score | Recap | 7 innings, run rule |
| 5/3/2009 | * | Middle Tennessee State | 6 | at | Troy | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | New Orleans | 5 | at | Florida Atlantic | 3 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | South Alabama |
| at | Louisiana-Monroe |
| Canceled | | Recap | CCD, inclement weather |
| West Coast Conference |
| 5/3/2009 |
| San Francisco | 4 | at | #16 Cal Poly | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | #30 San Diego | 4 | at | Loyola Marymount | 5 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | St. Mary's | 4 | at | Gonzaga | 6 | FINAL | Box Score | Recap | |
| 5/3/2009 |
| San Diego State | 4 | at | Santa Clara | 3 | FINAL | Box Score | Recap | |
| Western Athletic Conference |
| 5/3/2009 | * | Louisiana Tech | 8 | at | Hawaii | 7 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Nevada | 6 | at | Fresno State | 8 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | Nevada | 5 | at | Fresno State | 12 | FINAL | Box Score | Recap | 7 innings (makeup of 5/1 game) |
| 5/3/2009 | * | San Jose State | 10 | at | Sacramento State | 9 | FINAL | Box Score | Recap | |
| 5/3/2009 | * | San Jose State |
| at | Sacramento State |
| Canceled | | Recap | CCD, inclement weather (makeup of 5/1 game) |
| 5/3/2009 |
| Houston Baptist | 1 | at | New Mexico State | 4 | FINAL | Box Score | Recap | |