Italics indicate a traded pick.
| Round | Pick | Original Team | Current Team | Selection | Pos, '01 Team |
| 13 | 1 | Cincinnati | Cincinnati | Crawford, Paxton | P, Boston |
| 13 | 2 | San Francisco | San Francisco | Redman, Tike | OF, Pittsburgh |
| 13 | 3 | Toronto | Toronto | Hundley, Todd | C, Chicago (NL) |
| 13 | 4 | Cleveland | Cleveland | Bard, Josh | C, Cleveland |
| 13 | 5 | Montreal | Cleveland | Rolls, Damian | 2B, Tampa Bay |
| 13 | 6 | Boston | Boston | Bale, John | P, Baltimore |
| 13 | 7 | Milwaukee | Milwaukee | Meares, Pat | 2B, Pittsburgh |
| 13 | 8 | Baltimore | Baltimore | Cota, Humberto | C, Pittsburgh |
| 13 | 9 | Chicago (NL) | Chicago (NL) | Paniagua, Jose | P, Seattle |
| 13 | 10 | Texas | Texas | Brown, Adrian | OF, Pittsburgh |
| 13 | 11 | New York (AL) | New York (AL) | Torcato, Tony | 3B, San Francisco |
| 13 | 12 | Los Angeles | Los Angeles | Stephens, John | P, Baltimore |
| 13 | 13 | Houston | Houston | Hermansen, Chad | OF, Pittsburgh |
| 13 | 14 | Kansas City | Kansas City | Wise, Matt | P, Anaheim |
| 13 | 15 | Tampa Bay | Tampa Bay | Estalella, Bobby | C, New York (AL) |
| 13 | 16 | St. Louis | St. Louis | Martinez, Felix | 2B, Tampa Bay |
| 13 | 17 | Colorado | Colorado | Sanchez, Jesus | P, Florida |
| 13 | 18 | Seattle | Seattle | Alvarez, Wilson | P, Tampa Bay |
| 13 | 19 | New York (NL) | New York (NL) | Coolbaugh, Mike | 3B, Milwaukee |
| 13 | 20 | Minnesota | Minnesota | Santana, Johan | P, Minnesota |
| 13 | 21 | Detroit | Cincinnati | Machado, Robert | C, Chicago (NL) |
| 13 | 22 | Pittsburgh | Pittsburgh | Ellis, Mark | SS, Oakland |
| 13 | 23 | California | Boston | Coco, Pasqual | P, Toronto |
| 13 | 24 | Philadelphia | Philadelphia | Pena, Angel | C, Los Angeles |
| 14 | 1 | Cincinnati | New York (NL) | Cromer, D.T. | OF, Cincinnati |
| 14 | 2 | San Francisco | San Francisco | Monroe, Craig | OF, Texas |
| 14 | 3 | Cleveland | Cleveland | Butler, Brent | 2B, Colorado |
| 14 | 4 | Toronto | Philadelphia | Osuna, Antonio | P, Chicago (AL) |
| 14 | 5 | Montreal | Cleveland | Guzman, Edwards | C, San Francisco |
| 14 | 6 | Boston | Boston | Cooper, Brian | P, Anaheim |
| 14 | 7 | Baltimore | Baltimore | Eischen, Joey | P, Montreal |
| 14 | 8 | Milwaukee | Milwaukee | Arias, Alex | SS, San Diego |
| 14 | 9 | Chicago (NL) | Chicago (NL) | Jones, Todd | P, Minnesota |
| 14 | 10 | Texas | Texas | Moss, Damian | P, Atlanta |
| 14 | 11 | New York (AL) | New York (AL) | Mlicki, Dave | P, Houston |
| 14 | 12 | Los Angeles | Los Angeles | MacDougal, Mike | P, Kansas City |
| 14 | 13 | Houston | Houston | Lampkin, Tom | C, Seattle |
| 14 | 14 | Kansas City | Kansas City | White, Gabe | P, Colorado |
| 14 | 15 | Tampa Bay | Tampa Bay | Gil, Geronimo | C, Baltimore |
| 14 | 16 | St. Louis | St. Louis | Hackman, Luther | P, St. Louis |
| 14 | 17 | Colorado | Colorado | Echevarria, Angel | OF, Milwaukee |
| 14 | 18 | Seattle | Seattle | Rogers, Kenny | P, Texas |
| 14 | 19 | New York (NL) | New York (NL) | Berg, Dave | SS, Florida |
| 14 | 20 | Detroit | Detroit | Neal, Blaine | P, Florida |
| 14 | 21 | Minnesota | Minnesota | Reyes, Dennys | P, Cincinnati |
| 14 | 22 | Pittsburgh | Pittsburgh | Sabel, Erik | P, Arizona |
| 14 | 23 | California | Pittsburgh | Austin, Jeff | P, Kansas City |
| 14 | 24 | Philadelphia | San Francisco | Conti, Jason | OF, Arizona |
| 15 | 1 | Cincinnati | St. Louis | Suzuki, Mac | P, Milwaukee |
| 15 | 2 | San Francisco | Minnesota | Lunar, Fernando | C, Baltimore |
| 15 | 3 | Toronto | Toronto | Davis, Russ | 3B, San Francisco |
| 15 | 4 | Cleveland | Cleveland | Mackowiak, Rob | OF, Pittsburgh |
| 15 | 5 | Montreal | Cleveland | Bocachica, Hiram | 2B, Los Angeles |
| 15 | 6 | Boston | Boston | Eyre, Scott | P, Toronto |
| 15 | 7 | Milwaukee | Milwaukee | Gomes, Wayne | P, San Francisco |
| 15 | 8 | Baltimore | Baltimore | Cardona, Javier | C, Detroit |
| 15 | 9 | Chicago (NL) | Chicago (NL) | Berger, Brandon | OF, Kansas City |
| 15 | 10 | Texas | Texas | Roberts, Dave | OF, Cleveland |
| 15 | 11 | New York (AL) | New York (AL) | Castro, Ramon | C, Florida |
| 15 | 12 | Los Angeles | Los Angeles | Jensen, Ryan | P, San Francisco |
| 15 | 13 | Houston | Houston | McCarty, Dave | 1B, Kansas City |
| 15 | 14 | Kansas City | Kansas City | Bellhorn, Mark | 2B, Oakland |
| 15 | 15 | Tampa Bay | Tampa Bay | Serrano, Wascar | P, San Diego |
| 15 | 16 | St. Louis | St. Louis | Perez, Santiago | 2B, San Diego |
| 15 | 17 | Colorado | Colorado | Allen, Chad | OF, Minnesota |
| 15 | 18 | Seattle | Seattle | Martin, Al | OF, Seattle |
| 15 | 19 | New York (NL) | New York (NL) | Bako, Paul | C, Atlanta |
| 15 | 20 | Minnesota | Minnesota | Kinney, Matt | P, Minnesota |
| 15 | 21 | Detroit | Detroit | Pratt, Todd | C, Philadelphia |
| 15 | 22 | Pittsburgh | Pittsburgh | Johnson, Mark P. | 1B, New York (NL) |
| 15 | 23 | California | Pittsburgh | Latham, Chris | OF, Toronto |
| 15 | 24 | Philadelphia | Philadelphia | Barajas, Rod | C, Arizona |
| 16 | 1 | Cincinnati | St. Louis | Valentin, John | SS, Boston |
| 16 | 2 | San Francisco | San Francisco | Raines Jr., Tim | OF, Baltimore |
| 16 | 3 | Cleveland | Cleveland | Julio, Jorge | P, Baltimore |
| 16 | 4 | Toronto | Toronto | MacRae, Scott | P, Cincinnati |
| 16 | 5 | Montreal | Cleveland | Voyles, Brad | P, Kansas City |
| 16 | 6 | Boston | Boston | Sanchez, Alex | OF, Milwaukee |
| 16 | 7 | Baltimore | Baltimore | Marte, Damaso | P, Pittsburgh |
| 16 | 8 | Milwaukee | Milwaukee | Wasdin, John | P, Baltimore |
| 16 | 9 | Chicago (NL) | Chicago (NL) | Stark, Denny | P, Seattle |
| 16 | 10 | Texas | Texas | Walker, Kevin | P, San Diego |
| 16 | 11 | New York (AL) | New York (AL) | Merced, Orlando | OF, Houston |
| 16 | 12 | Los Angeles | Los Angeles | Benoit, Joaquin | P, Texas |
| 16 | 13 | Houston | Houston | Kim, Sun-Woo | P, Boston |
| 16 | 14 | Kansas City | Kansas City | Perez, Timo | OF, New York (NL) |
| 16 | 15 | Tampa Bay | Tampa Bay | Mattes, Troy | P, Montreal |
| 16 | 16 | St. Louis | St. Louis | Douglass, Sean | P, Baltimore |
| 16 | 17 | Colorado | Colorado | Taylor, Reggie | OF, Philadelphia |
| 16 | 18 | Seattle | Seattle | Burba, Dave | P, Cleveland |
| 16 | 19 | New York (NL) | Colorado | Almonte, Erick | SS, New York (AL) |
| 16 | 20 | Detroit | Detroit | Mahomes, Pat | P, Texas |
| 16 | 21 | Minnesota | Minnesota | Smith, Mark | OF, Montreal |
| 16 | 22 | Pittsburgh | Cleveland | Rigdon, Paul | P, Milwaukee |
| 16 | 23 | California | Kansas City | Hinch, A.J. | C, Kansas City |
| 16 | 24 | Philadelphia | Philadelphia | Middlebrook, Jason | P, San Diego |