Italics indicate a traded pick.
| Round | Pick | Original Team | Current Team | Selection | Pos, '01 Team |
| 1 | 1 | Milwaukee | Milwaukee | Beckett, Josh | P, Florida |
| 1 | 2 | Cincinnati | Cincinnati | Betemit, Wilson | SS, Atlanta |
| 1 | 3 | New York (AL) | New York (AL) | Lopez, Felipe | SS, Toronto |
| 1 | 4 | San Francisco | San Francisco | Tankersley, Dennis | P, San Diego |
| 1 | 5 | Toronto | Toronto | Hinske, Eric | 3B, Oakland |
| 1 | 6 | Cleveland | Cleveland | Thomas, Brad | P, Minnesota |
| 1 | 7 | Montreal | Montreal | Batista, Miguel | P, Arizona |
| 1 | 8 | Boston | Montreal | Redding, Tim | P, Houston |
| 1 | 9 | Baltimore | Baltimore | Wells, Vernon | OF, Toronto |
| 1 | 10 | Chicago (NL) | Chicago (NL) | Lyon, Brandon | P, Toronto |
| 1 | 11 | Texas | Texas | Vasquez, Ramon | SS, San Diego |
| 1 | 12 | Los Angeles | Los Angeles | Towers, Josh | P, Baltimore |
| 1 | 13 | Houston | Houston | Spooneybarger, Tim | P, Atlanta |
| 1 | 14 | Kansas City | New York (AL) | Ibanez, Raul | OF, Kansas City |
| 1 | 15 | Tampa Bay | Cleveland | Traber, Billy | P, New York (NL) |
| 1 | 16 | St. Louis | California | Giles, Marcus | 2B, Atlanta |
| 1 | 17 | Colorado | San Francisco | Rauch, Jon | P, Chicago (AL) |
| 1 | 18 | Seattle | Seattle | Cust, Jack | 1B, Arizona |
| 1 | 19 | New York (NL) | Philadelphia | Williams, Dave | P, Pittsburgh |
| 1 | 20 | Minnesota | Minnesota | Wilson, Paul | P, Tampa Bay |
| 1 | 21 | Detroit | Detroit | Rivera, Juan | OF, New York (AL) |
| 1 | 22 | Pittsburgh | Pittsburgh | Johnson, Adam | P, Minnesota |
| 1 | 23 | California | Cleveland | Hillenbrand, Shea | 3B, Boston |
| 1 | 24 | Philadelphia | Tampa Bay | Reitsma, Chris | P, Cincinnati |
| 2 | 1 | Cincinnati | Cincinnati | Phelps, Josh | C, Toronto |
| 2 | 2 | San Francisco | San Francisco | Colome, Jesus | P, Tampa Bay |
| 2 | 3 | Cleveland | Cleveland | Anderson, Jimmy | P, Pittsburgh |
| 2 | 4 | Toronto | Toronto | Macias, Jose | 2B, Detroit |
| 2 | 5 | Montreal | Montreal | Singleton, Chris | OF, Chicago (AL) |
| 2 | 6 | Boston | California | Ramos, Mario | P, Oakland |
| 2 | 7 | Baltimore | Baltimore | Hudson, Orlando | 2B, Toronto |
| 2 | 8 | Milwaukee | Milwaukee | Byrnes, Eric | OF, Oakland |
| 2 | 9 | Chicago (NL) | Chicago (NL) | D'Amico, Jeff | P, Milwaukee |
| 2 | 10 | Texas | Cincinnati | German, Esteban | 2B, Oakland |
| 2 | 11 | New York (AL) | New York (AL) | Hiljus, Erik | P, Oakland |
| 2 | 12 | Los Angeles | Los Angeles | Glover, Gary | P, Chicago (AL) |
| 2 | 13 | Houston | Houston | Sierra, Ruben | OF, Texas |
| 2 | 14 | Kansas City | New York (AL) | Velarde, Randy | 2B, New York (AL) |
| 2 | 15 | Tampa Bay | Tampa Bay | Phelps, Travis | P, Tampa Bay |
| 2 | 16 | St. Louis | Cincinnati | Strickland, Scott | P, Montreal |
| 2 | 17 | Colorado | San Francisco | Rapp, Pat | P, Anaheim |
| 2 | 18 | Seattle | Seattle | Rowand, Aaron | OF, Chicago (AL) |
| 2 | 19 | New York (NL) | New York (NL) | Coggin, Dave | P, Philadelphia |
| 2 | 20 | Detroit | Detroit | Hollandsworth, Todd | OF, Colorado |
| 2 | 21 | Minnesota | Minnesota | Roberts, Willis | P, Baltimore |
| 2 | 22 | Pittsburgh | Pittsburgh | Lackey, John | P, Anaheim |
| 2 | 23 | California | Montreal | Javier, Stan | OF, Seattle |
| 2 | 24 | Philadelphia | Philadelphia | Matthews, Mike | P, St. Louis |
| 3 | 1 | Cincinnati | Cincinnati | Charlton, Norm | P, Seattle |
| 3 | 2 | San Francisco | San Francisco | Perez, Tomas | 2B, Philadelphia |
| 3 | 3 | Toronto | Toronto | Clark, Brady | OF, Cincinnati |
| 3 | 4 | Cleveland | Boston | Lincoln, Mike | P, Pittsburgh |
| 3 | 5 | Montreal | Montreal | Smith, Chuck | P, Florida |
| 3 | 6 | Boston | Boston | Leiter, Mark | P, Milwaukee |
| 3 | 7 | Milwaukee | Milwaukee | Lima, Jose | P, Detroit |
| 3 | 8 | Baltimore | Baltimore | Zambrano, Victor | P, Tampa Bay |
| 3 | 9 | Chicago (NL) | New York (NL) | Figueroa, Nelson | P, Philadelphia |
| 3 | 10 | Texas | Texas | Perez, Odalis | P, Atlanta |
| 3 | 11 | New York (AL) | Kansas City | Inge, Brandon | C, Detroit |
| 3 | 12 | Los Angeles | Los Angeles | Bautista, Danny | OF, Arizona |
| 3 | 13 | Houston | Houston | Rupe, Ryan | P, Tampa Bay |
| 3 | 14 | Kansas City | Kansas City | Estrada, Johnny | C, Philadelphia |
| 3 | 15 | Tampa Bay | Tampa Bay | Feliz, Pedro | 3B, San Francisco |
| 3 | 16 | St. Louis | New York (AL) | Spiezio, Scott | 1B, Anaheim |
| 3 | 17 | Colorado | Colorado | Hentgen, Pat | P, Toronto |
| 3 | 18 | Seattle | Seattle | Chacon, Shawn | P, Colorado |
| 3 | 19 | New York (NL) | Cleveland | Fossum, Casey | P, Boston |
| 3 | 20 | Minnesota | Minnesota | Jackson, Mike | P, Houston |
| 3 | 21 | Detroit | Detroit | Davis, Lance | P, Cincinnati |
| 3 | 22 | Pittsburgh | Cleveland | Munson, Eric | 1B, Detroit |
| 3 | 23 | California | California | Fikac, Jeremy | P, San Diego |
| 3 | 24 | Philadelphia | Philadelphia | Spivey, Junior | 2B, Arizona |
| 4 | 1 | Cincinnati | Cincinnati | Seanez, Rudy | P, Atlanta |
| 4 | 2 | San Francisco | San Francisco | Beimel, Joe | P, Pittsburgh |
| 4 | 3 | Cleveland | Philadelphia | Mirabelli, Doug | C, Boston |
| 4 | 4 | Toronto | Toronto | Haynes, Jimmy | P, Milwaukee |
| 4 | 5 | Montreal | Montreal | Hernandez, Orlando | P, New York (AL) |
| 4 | 6 | Boston | Boston | Mohr, Dustan | OF, Minnesota |
| 4 | 7 | Baltimore | Tampa Bay | Weber, Ben | P, Anaheim |
| 4 | 8 | Milwaukee | Milwaukee | Williamson, Scott | P, Cincinnati |
| 4 | 9 | Chicago (NL) | Chicago (NL) | Bell, Jay | 2B, Arizona |
| 4 | 10 | Texas | Texas | Neagle, Denny | P, Colorado |
| 4 | 11 | New York (AL) | Baltimore | Marrero, Eli | C, St. Louis |
| 4 | 12 | Los Angeles | Los Angeles | Rios, Armando | OF, Pittsburgh |
| 4 | 13 | Houston | Houston | Tucker, Michael | OF, Chicago (NL) |
| 4 | 14 | Kansas City | Kansas City | Stairs, Matt | 1B, Chicago (NL) |
| 4 | 15 | Tampa Bay | New York (NL) | Quantrill, Paul | P, Toronto |
| 4 | 16 | St. Louis | Cincinnati | Zaun, Gregg | C, Florida |
| 4 | 17 | Colorado | Colorado | Carrara, Giovanni | P, Los Angeles |
| 4 | 18 | Seattle | Seattle | Blum, Geoff | 3B, Montreal |
| 4 | 19 | New York (NL) | Chicago (NL) | Jenning, Jason | P, Colorado |
| 4 | 20 | Detroit | Detroit | Palmer, Dean | DH, Detroit |
| 4 | 21 | Minnesota | Minnesota | Ryan, B.J. | P, Baltimore |
| 4 | 22 | Pittsburgh | Pittsburgh | Dellucci, David | OF, Arizona |
| 4 | 23 | California | California | Choate, Randy | P, New York (AL) |
| 4 | 24 | Philadelphia | Toronto | Drese, Ryan | P, Cleveland |