Italics indicate a traded pick.
| Round | Pick | Original Team | Current Team | Selection | Pos, '01 Team |
| 9 | 1 | Cincinnati | Cincinnati | O'Leary, Troy | OF, Boston |
| 9 | 2 | San Francisco | San Francisco | Buddie, Mike | P, Milwaukee |
| 9 | 3 | Toronto | Toronto | Bichette, Dante | OF, Boston |
| 9 | 4 | Cleveland | Texas | Miller, Corky | C, Cincinnati |
| 9 | 5 | Montreal | Montreal | Darensbourg, Vic | P, Florida |
| 9 | 6 | Boston | Boston | Guillen, Jose | OF, Tampa Bay |
| 9 | 7 | Milwaukee | FORFEIT | ||
| 9 | 8 | Baltimore | Baltimore | Wright, Dan | P, Chicago (AL) |
| 9 | 9 | Chicago (NL) | Chicago (NL) | Holt, Chris | P, Detroit |
| 9 | 10 | Texas | Texas | Timlin, Mike | P, St. Louis |
| 9 | 11 | New York (AL) | New York (AL) | Wallace, Jeff | P, Tampa Bay |
| 9 | 12 | Los Angeles | Los Angeles | Ginter, Keith | 2B, Houston |
| 9 | 13 | Houston | Houston | Plesac, Dan | P, Toronto |
| 9 | 14 | Kansas City | Kansas City | Guthrie, Mark | P, Oakland |
| 9 | 15 | Tampa Bay | New York (NL) | Fultz, Aaron | P, San Francisco |
| 9 | 16 | St. Louis | Cincinnati | Strange, Pat | P, New York (NL) |
| 9 | 17 | Colorado | FORFEIT | ||
| 9 | 18 | Seattle | Seattle | Tomko, Brett | P, Seattle |
| 9 | 19 | New York (NL) | New York (NL) | Sprague, Ed | 3B, Seattle |
| 9 | 20 | Minnesota | Minnesota | Arroyo, Bronson | P, Pittsburgh |
| 9 | 21 | Detroit | Texas | Padilla, Vicente | P, Philadelphia |
| 9 | 22 | Pittsburgh | Pittsburgh | Cormier, Rheal | P, Philadelphia |
| 9 | 23 | California | California | Boehringer, Brian | P, San Francisco |
| 9 | 24 | Philadelphia | Philadelphia | Derosa, Mark | SS, Atlanta |
| 10 | 1 | Cincinnati | Cincinnati | Dunston, Shawon | OF, San Francisco |
| 10 | 2 | San Francisco | San Francisco | Bradford, Chad | P, Oakland |
| 10 | 3 | Cleveland | California | Rincon, Juan | P, Minnesota |
| 10 | 4 | Toronto | Texas | Rivera, Mike | C, Detroit |
| 10 | 5 | Montreal | Texas | Payton, Jay | OF, New York (NL) |
| 10 | 6 | Boston | Boston | Gant, Ron | OF, Oakland |
| 10 | 7 | Baltimore | Baltimore | Cairo, Miguel | 3B, St. Louis |
| 10 | 8 | Milwaukee | FORFEIT | ||
| 10 | 9 | Chicago (NL) | Chicago (NL) | Gonzalez, Dicky | P, New York (NL) |
| 10 | 10 | Texas | Texas | Nunez, Jose Antonio | P, San Diego |
| 10 | 11 | New York (AL) | New York (AL) | Calloway, Ron | OF, Montreal |
| 10 | 12 | Los Angeles | FORFEIT | ||
| 10 | 13 | Houston | Houston | Flaherty, John | C, Tampa Bay |
| 10 | 14 | Kansas City | Kansas City | Ripken Jr., Cal | 3B, Baltimore |
| 10 | 15 | Tampa Bay | Tampa Bay | Myette, Aaron | P, Texas |
| 10 | 16 | St. Louis | St. Louis | Deshields, Delino | OF, Chicago (NL) |
| 10 | 17 | Colorado | FORFEIT | ||
| 10 | 18 | Seattle | Seattle | Hammonds, Jeffrey | OF, Milwaukee |
| 10 | 19 | New York (NL) | New York (NL) | Valent, Eric | OF, Philadelphia |
| 10 | 20 | Detroit | Detroit | Martinez, Dave | OF, Atlanta |
| 10 | 21 | Minnesota | Minnesota | Castro, Juan | 2B, Cincinnati |
| 10 | 22 | Pittsburgh | Pittsburgh | Bottalico, Ricky | OF, Philadelphia |
| 10 | 23 | California | California | Gautreau, Jake | 2B, San Diego |
| 10 | 24 | Philadelphia | Philadelphia | Riggan, Jerrod | P, New York (NL) |
| 11 | 1 | Cincinnati | Cincinnati | Roberts, Grant | P, New York (NL) |
| 11 | 2 | San Francisco | San Francisco | Kielty, Bobby | OF, Minnesota |
| 11 | 3 | Toronto | Toronto | Rodriguez, Rich | P, Cleveland |
| 11 | 4 | Cleveland | Toronto | Zerbe, Chad | P, San Francisco |
| 11 | 5 | Montreal | Detroit | Nunez, Abraham | SS, Pittsburgh |
| 11 | 6 | Boston | Boston | Fogg, Josh | P, Chicago (AL) |
| 11 | 7 | Milwaukee | Milwaukee | Goodwin, Tom | OF, Los Angeles |
| 11 | 8 | Baltimore | Baltimore | Lopez, Luis (MIL) | SS, Milwaukee |
| 11 | 9 | Chicago (NL) | New York (NL) | Romano, Jason | 2B, Texas |
| 11 | 10 | Texas | Texas | Santiago, Jose | P, Philadelphia |
| 11 | 11 | New York (AL) | New York (AL) | Robinson, Kerry | OF, St. Louis |
| 11 | 12 | Los Angeles | Los Angeles | Ortega, Bill | OF, St. Louis |
| 11 | 13 | Houston | Houston | Gardner, Mark | P, San Francisco |
| 11 | 14 | Kansas City | Kansas City | Bauer, Rick | P, Baltimore |
| 11 | 15 | Tampa Bay | Tampa Bay | Pickering, Calvin | 1B, Boston |
| 11 | 16 | St. Louis | St. Louis | Cora, Alex | SS, Los Angeles |
| 11 | 17 | Colorado | Colorado | Olsen, Kevin | P, Florida |
| 11 | 18 | Seattle | Seattle | Ojeda, Augie | SS, Chicago (NL) |
| 11 | 19 | New York (NL) | New York (NL) | Rodriguez, Wilfredo | P, Houston |
| 11 | 20 | Minnesota | Minnesota | Wohlers, Mark | P, New York (AL) |
| 11 | 21 | Detroit | Detroit | Ludwick, Ryan | OF, Oakland |
| 11 | 22 | Pittsburgh | California | Parris, Steve | P, Toronto |
| 11 | 23 | California | California | Romero, J.C. | P, Minnesota |
| 11 | 24 | Philadelphia | Philadelphia | Duncan, Courtney | P, Chicago (NL) |
| 12 | 1 | Cincinnati | Cincinnati | Hansen, Dave | 3B, Los Angeles |
| 12 | 2 | San Francisco | San Francisco | Harris, Willie | OF, Baltimore |
| 12 | 3 | Cleveland | Toronto | Saenz, Olmedo | 3B, Oakland |
| 12 | 4 | Toronto | Toronto | Hamilton, Joey | P, Cincinnati |
| 12 | 5 | Montreal | Detroit | Overbay, Lyle | 1B, Arizona |
| 12 | 6 | Boston | Boston | Politte, Cliff | P, Philadelphia |
| 12 | 7 | Baltimore | Baltimore | Villone, Ron | P, Houston |
| 12 | 8 | Milwaukee | Milwaukee | Sadler, Donnie | 2B, Kansas City |
| 12 | 9 | Chicago (NL) | Chicago (NL) | Elarton, Scott | P, Colorado |
| 12 | 10 | Texas | Texas | Davis, Kane | P, Colorado |
| 12 | 11 | New York (AL) | New York (AL) | Merloni, Lou | SS, Boston |
| 12 | 12 | Los Angeles | Los Angeles | Encarnacion, Mario | OF, Colorado |
| 12 | 13 | Houston | Houston | Carrasco, Hector | P, Minnesota |
| 12 | 14 | Kansas City | Kansas City | Hitchcock, Sterling | P, New York (AL) |
| 12 | 15 | Tampa Bay | Tampa Bay | Colangelo, Mike | OF, San Diego |
| 12 | 16 | St. Louis | St. Louis | Roberts, Brian | 2B, Baltimore |
| 12 | 17 | Colorado | Colorado | Haselman, Bill | C, Texas |
| 12 | 18 | Seattle | Seattle | Riske, David | P, Cleveland |
| 12 | 19 | New York (NL) | New York (NL) | Ortiz, Hector | C, Kansas City |
| 12 | 20 | Detroit | Detroit | Ledee, Ricky | OF, Texas |
| 12 | 21 | Minnesota | Minnesota | Creek, Doug | P, Tampa Bay |
| 12 | 22 | Pittsburgh | California | Wilson, Vance | C, New York (NL) |
| 12 | 23 | California | Cleveland | Olivares, Omar | P, Pittsburgh |
| 12 | 24 | Philadelphia | Toronto | Rijo, Jose | P, Cincinnati |