| Amateur draft (18) | ||
| Player | Year | Round |
| John Grabow | 1997 | 3rd |
| Mike Johnston | 1998 | 20th |
| Ryan Doumit | 1999 | 2nd |
| Sean Burnett | 2000 | 1st |
| *-Jose Bautista | 2000 | 20th |
| Nate McLouth | 2000 | 25th |
| Ian Snell | 2000 | 26th |
| John Van Benschoten | 2001 | 1st |
| Chris Duffy | 2001 | 8th |
| Zach Duke | 2001 | 20th |
| Rajai Davis | 2001 | 38th |
| Bryan Bullington | 2002 | 1st |
| Brad Eldred | 2002 | 6th |
| Matt Capps | 2002 | 7th |
| Paul Maholm | 2003 | 1st |
| Tom Gorzelanny | 2003 | 2nd |
| Craig Stansberry | 2003 | 5th |
| Josh Sharpless | 2003 | 24th |
| International signings (3) | ||
| Player | Year | Country |
| Jose Castillo | 1997 | Venezuela |
| *-Ronny Paulino | 1997 | Dominican |
| Javier Guzman | 2000 | Dominican |
| Major-league free agents (3) | ||
| Player | Year | Term |
| Roberto Hernandez | 2005 | 1-$2.75 |
| Joe Randa | 2005 | 1-$4.00 |
| Jeromy Burnitz | 2006 | 1-$6.00 |
| Term: Year(s)-millions of dollars | ||
| Minor-league free agents (1) | ||
| Player | Year | Term |
| Salomon Torres | 2002 | 1-$325,000 |
| Jose Hernandez | 2006 | 1-$850,000 |
| Term: Year(s)-dollars | ||
| Trades (13) | ||
| Player | Year | From |
| Craig Wilson | 1996 | Toronto |
| Humberto Cota | 1999 | Tampa Bay |
| Jack Wilson | 2000 | St. Louis |
| Ryan Vogelsong | 2001 | San Francisco |
| Kip Wells | 2001 | Chicago (AL) |
| Jason Bay | 2003 | San Diego |
| Oliver Perez | 2003 | San Diego |
| Mike Gonzalez | 2003 | Boston |
| Freddy Sanchez | 2003 | Boston |
| Jody Gerut | 2005 | Chicago (NL) |
| Jonah Bayliss | 2005 | Kansas City |
| Sean Casey | 2005 | Cincinnati |
| Damaso Marte | 2005 | Chicago (AL) |
| Rule 5 draft picks (2) | ||
| Player | Year | From |
| Yurendell DeCaster | 2000 | Tampa Bay |
| Victor Santos | 2005 | Kansas City |
-Spent less than a season with another organization through Rule 5 but was reacquired.