Italics indicate a traded pick.
| Round | Pick | Original Team | Current Team | Selection | Pos, '01 Team |
| 5 | 1 | Cincinnati | Cincinnati | Mora, Melvin | CF, Baltimore |
| 5 | 2 | San Francisco | San Francisco | Trombley, Mike | P, Los Angeles |
| 5 | 3 | Toronto | Toronto | Powell, Jay | P, Colorado |
| 5 | 4 | Cleveland | New York (AL) | Byrd, Paul | P, Kansas City |
| 5 | 5 | Montreal | Montreal | Loaiza, Esteban | P, Toronto |
| 5 | 6 | Boston | Boston | Ohka, Tomo | P, Montreal |
| 5 | 7 | Milwaukee | Milwaukee | Guerrier, Matt | P, Chicago (AL) |
| 5 | 8 | Baltimore | Baltimore | Snow, J.T. | 1B, San Francisco |
| 5 | 9 | Chicago (NL) | Chicago (NL) | Surhoff, B.J. | OF, Atlanta |
| 5 | 10 | Texas | New York (AL) | Norton, Greg | 1B, Colorado |
| 5 | 11 | New York (AL) | Kansas City | Lansing, Mike | SS, Boston |
| 5 | 12 | Los Angeles | Los Angeles | Galarraga, Andres | 1B, San Francisco |
| 5 | 13 | Houston | Houston | Lohse, Kyle | P, Minnesota |
| 5 | 14 | Kansas City | Kansas City | Anderson, Brian | P, Arizona |
| 5 | 15 | Tampa Bay | Tampa Bay | Acevedo, Jose | P, Cincinnati |
| 5 | 16 | St. Louis | California | Prinz, Bret | P, Arizona |
| 5 | 17 | Colorado | Colorado | Darr, Mike | OF, San Diego |
| 5 | 18 | Seattle | Seattle | Chiasson, Scott | P, Chicago (NL) |
| 5 | 19 | New York (NL) | New York (NL) | Mercado, Hector | P, Cincinnati |
| 5 | 20 | Minnesota | San Francisco | Little, Mark | OF, Colorado |
| 5 | 21 | Detroit | Detroit | Bierbrodt, Nick | P, Tampa Bay |
| 5 | 22 | Pittsburgh | Pittsburgh | Stewart, Scott | P, Montreal |
| 5 | 23 | California | California | Moreno, Juan | P, Texas |
| 5 | 24 | Philadelphia | Philadelphia | Helms, Wes | 1B, Atlanta |
| 6 | 1 | Cincinnati | Cincinnati | Graffanino, Tony | 2B, Chicago (AL) |
| 6 | 2 | San Francisco | Minnesota | Grissom, Marquis | OF, Los Angeles |
| 6 | 3 | Cleveland | Philadelphia | Redman, Mark | P, Minnesota |
| 6 | 4 | Toronto | Tampa Bay | Lilly, Ted | P, New York (AL) |
| 6 | 5 | Montreal | Montreal | Mordecai, Mike | 3B, Montreal |
| 6 | 6 | Boston | Boston | Eusebio, Tony | C, Houston |
| 6 | 7 | Baltimore | Baltimore | Santos, Victor | P, Detroit |
| 6 | 8 | Milwaukee | Milwaukee | Vizcaino, Jose | SS, Houston |
| 6 | 9 | Chicago (NL) | Chicago (NL) | Cone, David | P, Boston |
| 6 | 10 | Texas | California | Johnson, Russ | 2B, Tampa Bay |
| 6 | 11 | New York (AL) | New York (AL) | Buchanan, Brian | OF, Minnesota |
| 6 | 12 | Los Angeles | Los Angeles | Yoshii, Masato | P, Montreal |
| 6 | 13 | Houston | Houston | Mercedes, Jose | P, Baltimore |
| 6 | 14 | Kansas City | Kansas City | Franklin, Ryan | P, Seattle |
| 6 | 15 | Tampa Bay | Tampa Bay | Levrault, Allen | P, Milwaukee |
| 6 | 16 | St. Louis | California | Martinez, Ramon (SF) | 2B, San Francisco |
| 6 | 17 | Colorado | Colorado | Guerrero, Wilton | 2B, Cincinnati |
| 6 | 18 | Seattle | Seattle | Perry, Herbert | 1B, Chicago (AL) |
| 6 | 19 | New York (NL) | New York (NL) | Simon, Randall | 1B, Detroit |
| 6 | 20 | Detroit | Detroit | Biddle, Rocky | P, Chicago (AL) |
| 6 | 21 | Minnesota | Minnesota | Bergeron, Peter | OF, Montreal |
| 6 | 22 | Pittsburgh | Pittsburgh | Cressend, Jack | P, Minnesota |
| 6 | 23 | California | California | Thurman, Mike | P, Montreal |
| 6 | 24 | Philadelphia | Philadelphia | Christensen, McKay | OF, Los Angeles |
| 7 | 1 | Cincinnati | Cincinnati | Bailey, Cory | P, Kansas City |
| 7 | 2 | San Francisco | San Francisco | Hatteberg, Scott | C, Boston |
| 7 | 3 | Toronto | Toronto | Bordick, Mike | SS, Baltimore |
| 7 | 4 | Cleveland | California | King, Ray | P, Milwaukee |
| 7 | 5 | Montreal | Montreal | Lloyd, Graeme | P, Montreal |
| 7 | 6 | Boston | Boston | Sandberg, Jared | 3B, Tampa Bay |
| 7 | 7 | Milwaukee | Milwaukee | Harvey, Ken | 1B, Kansas City |
| 7 | 8 | Baltimore | Baltimore | Shumpert, Terry | 2B, Colorado |
| 7 | 9 | Chicago (NL) | Chicago (NL) | Fletcher, Darrin | C, Toronto |
| 7 | 10 | Texas | Texas | Wilson, Jack | SS, Pittsburgh |
| 7 | 11 | New York (AL) | New York (AL) | Alicea, Luis | 3B, Kansas City |
| 7 | 12 | Los Angeles | Los Angeles | Ellis, Robert | P, Arizona |
| 7 | 13 | Houston | Houston | Benard, Marvin | OF, San Francisco |
| 7 | 14 | Kansas City | Kansas City | Minor, Damon | 1B, San Francisco |
| 7 | 15 | Tampa Bay | Tampa Bay | Pettyjohn, Adam | P, Detroit |
| 7 | 16 | St. Louis | New York (NL) | Alomar Jr., Sandy | C, Chicago (AL) |
| 7 | 17 | Colorado | Colorado | Dreifort, Darren | P, Los Angeles |
| 7 | 18 | Seattle | Seattle | Lewis, Darren | OF, Boston |
| 7 | 19 | New York (NL) | New York (NL) | Mathews, T.J. | P, St. Louis |
| 7 | 20 | Minnesota | Minnesota | Fordyce, Brook | C, Baltimore |
| 7 | 21 | Detroit | Detroit | Young, Kevin | 1B, Pittsburgh |
| 7 | 22 | Pittsburgh | Pittsburgh | Borbon Jr., Pedro | P, Toronto |
| 7 | 23 | California | California | Garcia, Karim | OF, Cleveland |
| 7 | 24 | Philadelphia | Philadelphia | Valdez, Mario | 1B, Oakland |
| 8 | 1 | Cincinnati | Cincinnati | Hunter, Brian | OF, Philadelphia |
| 8 | 2 | San Francisco | San Francisco | Brown, Roosevelt | OF, Chicago (NL) |
| 8 | 3 | Cleveland | New York (NL) | Beck, Rod | P, Boston |
| 8 | 4 | Toronto | Toronto | Venafro, Mike | P, Texas |
| 8 | 5 | Montreal | Montreal | Christiansen, Jason | P, San Francisco |
| 8 | 6 | Boston | Boston | Swindell, Greg | P, Arizona |
| 8 | 7 | Baltimore | Baltimore | Truby, Chris | 3B, Houston |
| 8 | 8 | Milwaukee | Milwaukee | Mateo, Ruben | OF, Cincinnati |
| 8 | 9 | Chicago (NL) | Chicago (NL) | Stechschulte, Gene | P, St. Louis |
| 8 | 10 | Texas | Texas | Everett, Adam | SS, Houston |
| 8 | 11 | New York (AL) | New York (AL) | Myers, Greg | C, Oakland |
| 8 | 12 | Los Angeles | Los Angeles | Cabrera, Jolbert | 2B, Cleveland |
| 8 | 13 | Houston | Houston | Matthews Jr., Gary | OF, Pittsburgh |
| 8 | 14 | Kansas City | Kansas City | Goodwin, Tom | OF, Los Angeles |
| 8 | 15 | Tampa Bay | Chicago (NL) | Witasick, Jay | P, New York (AL) |
| 8 | 16 | St. Louis | St. Louis | Reames, Britt | P, Montreal |
| 8 | 17 | Colorado | Colorado | Michalak, Chris | P, Texas |
| 8 | 18 | Seattle | Seattle | Henderson, Rickey | OF, San Diego |
| 8 | 19 | New York (NL) | Texas | McKnight, Tony | P, Pittsburgh |
| 8 | 20 | Detroit | Detroit | Paul, Josh | C, Chicago (AL) |
| 8 | 21 | Minnesota | Minnesota | White, Rick | P, New York (NL) |
| 8 | 22 | Pittsburgh | Pittsburgh | Kinkade, Mike | 3B, Baltimore |
| 8 | 23 | California | California | Collier, Lou | OF, Milwaukee |
| 8 | 24 | Philadelphia | New York (NL) | Reboulet, Jeff | SS, Los Angeles |