| Draft Picks |
| Rd | # | Orig Team | # | Curr Team | Player | Overall |
| 1 | 1 | ST |   |   | Mark Mulder | 1 |
| 1 | 2 | VS |   |   | Freddy Garcia | 2 |
| | Transaction |   |   | CH released Ken Caminiti, Brady Anderson | |
| 1 | 3 | CH |   |   | Aubrey Huff | 3 |
| 1 | 4 | LZ |   |   | Michael Young | 4 |
| 1 | 5 | EM |   |   | Wade Miller | 5 |
| 1 | 6 | CA |   |   | C.C. Sabathia | 6 |
| 1 | 7 | GE |   |   | Jimmy Rollins | 7 |
| 1 | 8 | LI |   |   | Ben Sheets | 8 |
| 1 | 9 | HF |   | LZ | *Hideki Matsui* | 9 |
| 1 | 10 | HB |   |   | Jason Marquis | 10 |
| 1 | 11 | BV |   |   | Steve Trachsel | 11 |
| 1 | 12 | PE |   |   | Junior Spivey | 12 |
| 1 | 13 | KK |   |   | Marcus Giles, released Lou Merloni | 13 |
| 1 | 14 | PG |   |   | A.J. Pierzynski, released Brook Fordyce | 14 |
| 1 | 15 | WL |   |   | Billy Wagner | 15 |
| 1 | 16 | DM |   |   | Paul Abbott | 16 |
| 1 | 17 | SC |   | BV | Brad Wilkerson | 17 |
| 1 | 18 | EC |   |   | Vernon Wells | 18 |
| 1 | 19 | NI |   | DM | Richie Sexson | 19 |
| 1 | 20 | TR |   |   | Brian Lawrence | 20 |
| 2 | 1 | ST |   |   | Neifi Perez, released Fernando Tatis | 21 |
| 2 | 2 | VS |   |   | Carlos Guillen | 22 |
| 2 | 3 | CH |   |   | Corey Patterson | 23 |
| 2 | 4 | LZ |   | EC | Craig Wilson | 24 |
| 2 | 5 | EM |   |   | Juan Uribe | 25 |
| 2 | 6 | CA |   |   | Ugueth Urbina | 26 |
| 2 | 7 | GE |   |   | Nick Johnson, released Geoff Blum | 27 |
| 2 | 8 | LI |   |   | Aaron Rowand | 28 |
| 2 | 9 | HF |   |   | *Hank Blalock* | 29 |
| 2 | 10 | HB |   |   | John Thomson | 30 |
| 2 | 11 | BV |   |   | Juan Cruz | 31 |
| 2 | 12 | PE |   |   | Steve Sparks | 32 |
| 2 | 13 | KK |   |   | Vinny Castilla, released Denny Hocking | 33 |
| 2 | 14 | PG |   |   | Elmer Dessens, released Jeff D'Amico | 34 |
| 2 | 15 | WL |   |   | Ryan Franklin | 35 |
| 2 | 16 | DM |   |   | Jose Ortiz | 36 |
| 2 | 17 | SC |   |   | Jeff Cirillo | 37 |
| 2 | 18 | EC |   |   | Ruben Sierra | 38 |
| 2 | 19 | NI |   |   | *Carlos Zambrano* | 39 |
| 2 | 20 | TR |   |   | *Dontrelle Willis*, released Deivi Cruz | 40 |
| | Trade |   |   | ST trade Rick Helling and ST 5th pick to NI for 4 points | |
| 3 | 1 | ST |   |   | *Carl Crawford*, released Mike Mordecai | 41 |
| 3 | 2 | VS |   |   | Doug Mientkiewicz | 42 |
| 3 | 3 | CH |   |   | Johnny Estrada, released Jose Offerman | 43 |
| 3 | 4 | LZ |   | DM | Daryle Ward | 44 |
| 3 | 5 | EM |   |   | Shea Hillenbrand | 45 |
| 3 | 6 | CA |   |   | Marty Cordova | 46 |
| 3 | 7 | GE |   |   | Mark Bellhorn, released Mark McGwire | 47 |
| 3 | 8 | LI |   |   | Dan Wilson | 48 |
| 3 | 9 | HF |   |   | Ted Lilly, released Doug Henry | 49 |
| 3 | 10 | HB |   |   | Ben Weber | 50 |
| 3 | 11 | BV |   |   | Guillermo Mota | 51 |
| 3 | 12 | PE |   |   | Cesar Izturis | 52 |
| 3 | 13 | KK |   |   | Rolando Arrojo, released John Halama | 53 |
| 3 | 14 | PG |   |   | Tomas Perez | 54 |
| 3 | 15 | WL |   |   | Flash Gordon | 55 |
| 3 | 16 | DM |   |   | Dean Palmer | 56 |
| 3 | 17 | SC |   |   | Victor Zambrano | 57 |
| 3 | 18 | EC |   |   | Damaso Marte, released Donne Wall | 58 |
| 3 | 19 | NI |   | EC | Chad Bradford | 59 |
| 3 | 20 | TR |   |   | Michael Barrett, released Sandy Alomar | 60 |
| 4 | 1 | ST |   |   | Ray King | 61 |
| 4 | 2 | VS |   |   | Stan Javier | 62 |
| 4 | 3 | CH |   |   | Jason Christiansen, released Justin Speier | 63 |
| 4 | 4 | LZ |   |   | | 64 |
| 4 | 5 | EM |   |   | Danny Patterson | 65 |
| 4 | 6 | CA |   |   | | 66 |
| 4 | 7 | GE |   |   | Danys Baez, released Lou Pote | 67 |
| 4 | 8 | LI |   |   | Ricardo Rincon | 68 |
| 4 | 9 | HF |   |   | Jack Wilson | 69 |
| 4 | 10 | HB |   |   | D'Angelo Jimenez | 70 |
| 4 | 11 | BV |   |   | | 71 |
| 4 | 12 | PE |   |   | Russ Johnson | 72 |
| 4 | 13 | KK |   |   | Alex Cora, released Jermaine Dye | 73 |
| 4 | 14 | PG |   |   | Tony Gwynn, released Ruben Mateo | 74 |
| 4 | 15 | WL |   |   | Miguel Cairo | 75 |
| 4 | 16 | DM |   |   | Brandon Duckworth | 76 |
| 4 | 17 | SC |   |   | Sean Lowe | 77 |
| 4 | 18 | EC |   |   | Damian Jackson, released Jeff Frye | 78 |
| 4 | 19 | NI |   |   | Mark DeRosa, released Terry Shumpert | 79 |
| 4 | 20 | TR |   |   | Rob Mackowiak, released Brad Fullmer | 80 |
| 5 | 1 | ST |   | NI | Jeff Zimmerman, released Rick Helling | 81 |
| 5 | 2 | VS |   |   | Giovanni Carrara | 82 |
| 5 | 3 | CH |   |   | Mike Matthews, released John Mabry | 83 |
| 5 | 4 | LZ |   |   | | 84 |
| 5 | 5 | EM |   |   | | 85 |
| 5 | 6 | CA |   |   | | 86 |
| 5 | 7 | GE |   |   | | 87 |
| 5 | 8 | LI |   |   | | 88 |
| 5 | 9 | HF |   |   | Norm Charlton, released Pat Hentgen | 89 |
| 5 | 10 | HB |   |   | Julio Franco | 90 |
| 5 | 11 | BV |   |   | | 91 |
| 5 | 12 | PE |   | BV | | 92 |
| 5 | 13 | KK |   |   | | 93 |
| 5 | 14 | PG |   |   | Jermaine Dye, released Chris Richard | 94 |
| 5 | 15 | WL |   |   | Toby Hall | 95 |
| 5 | 16 | DM |   |   | Wiki Gonzalez | 96 |
| 5 | 17 | SC |   |   | Tom Prince | 97 |
| 5 | 18 | EC |   |   | Terry Shumpert, released Keith Osik | 98 |
| 5 | 19 | NI |   |   | Chad Fox, released Rusty Greer | 99 |
| 5 | 20 | TR |   |   | | 100 |
| 6 | 1 | ST |   |   | | 101 |
| 6 | 2 | VS |   |   | Luis Matos | 102 |
| 6 | 3 | CH |   |   | Ronnie Belliard, released Chris Stynes | 103 |
| 6 | 4 | LZ |   |   | | 104 |
| 6 | 5 | EM |   |   | | 105 |
| 6 | 6 | CA |   |   | | 106 |
| 6 | 7 | GE |   |   | | 107 |
| 6 | 8 | LI |   |   | | 108 |
| 6 | 9 | HF |   |   | | 109 |
| 6 | 10 | HB |   |   | Einar Diaz | 110 |
| 6 | 11 | BV |   |   | | 111 |
| 6 | 12 | PE |   |   | Chad Kreuter | 112 |
| 6 | 13 | KK |   |   | | 113 |
| 6 | 14 | PG |   |   | Luis Rivas, released Delino DeShields | 114 |
| 6 | 15 | WL |   |   | Dave Williams | 115 |
| 6 | 16 | DM |   |   | Jeff Shaw, released Omar Daal | 116 |
| 6 | 17 | SC |   |   | | 117 |
| 6 | 18 | EC |   |   | Chris Singleton, released Mike Hampton | 118 |
| | Trade |   |   | NI trade Richard Hidalgo, 4th pick in 2003, | |
| | |   |   | 5th pick in 2004 to EC for 3rd pick in 2003 | |
| | Transaction |   |   | EC released Pedro Borbon | |
| 6 | 19 | NI |   |   | John Riedling | 119 |
| 6 | 20 | TR |   |   | | 120 |
| 7 | 1 | ST |   |   | | 121 |
| 7 | 2 | VS |   |   | | 122 |
| 7 | 3 | CH |   |   | *Mark Teixeira*, released Greg Colbrunn | 123 |
| 7 | 4 | LZ |   |   | | 124 |
| 7 | 5 | EM |   |   | | 125 |
| 7 | 6 | CA |   |   | | 126 |
| 7 | 7 | GE |   |   | | 127 |
| 7 | 8 | LI |   |   | | 128 |
| 7 | 9 | HF |   |   | Mike Hampton, released Jerry Hairston | 129 |
| 7 | 10 | HB |   |   | David Dellucci | 130 |
| 7 | 11 | BV |   |   | | 131 |
| 7 | 12 | PE |   |   | Devon White | 132 |
| 7 | 13 | KK |   |   | | 133 |
| 7 | 14 | PG |   |   | Omar Daal, released Denny Neagle | 134 |
| 7 | 15 | WL |   |   | Randy Winn | 135 |
| 7 | 16 | DM |   |   | Tony Womack, released Jose Vizcaino | 136 |
| 7 | 17 | SC |   |   | | 137 |
| 7 | 18 | EC |   |   | Mike Lincoln, released Dave Veres | 138 |
| 7 | 19 | NI |   |   | | 139 |
| 7 | 20 | TR |   |   | | 140 |
| 8 | 1 | ST |   |   | | 141 |
| 8 | 2 | VS |   |   | | 142 |
| 8 | 3 | CH |   |   | Travis Lee, released Todd Hundley | 143 |
| 8 | 4 | LZ |   | NI | | 144 |
| 8 | 5 | EM |   |   | | 145 |
| 8 | 6 | CA |   |   | | 146 |
| 8 | 7 | GE |   |   | | 147 |
| 8 | 8 | LI |   |   | | 148 |
| 8 | 9 | HF |   |   | | 149 |
| 8 | 10 | HB |   |   | | 150 |
| 8 | 11 | BV |   |   | | 151 |
| 8 | 12 | PE |   |   | | 152 |
| 8 | 13 | KK |   |   | | 153 |
| 8 | 14 | PG |   |   | Randy Choate, released John Franco | 154 |
| 8 | 15 | WL |   |   | Joe Kennedy | 155 |
| 8 | 16 | DM |   |   | Ben Molina, released Brent Mayne | 156 |
| 8 | 17 | SC |   |   | | 157 |
| 8 | 18 | EC |   |   | *Oliver Perez* | 158 |
| 8 | 19 | NI |   |   | | 159 |
| 8 | 20 | TR |   |   | | 160 |
| 9 | 1 | ST |   |   | | 161 |
| 9 | 2 | VS |   |   | | 162 |
| 9 | 3 | CH |   |   | | 163 |
| 9 | 4 | LZ |   |   | | 164 |
| 9 | 5 | EM |   |   | | 165 |
| 9 | 6 | CA |   |   | | 166 |
| 9 | 7 | GE |   |   | | 167 |
| 9 | 8 | LI |   |   | | 168 |
| 9 | 9 | HF |   |   | | 169 |
| 9 | 10 | HB |   |   | | 170 |
| 9 | 11 | BV |   |   | | 171 |
| 9 | 12 | PE |   |   | | 172 |
| 9 | 13 | KK |   |   | | 173 |
| 9 | 14 | PG |   |   | Matt Herges, released Rick White | 174 |
| 9 | 15 | WL |   |   | Brian Daubach | 175 |
| 9 | 16 | DM |   |   | | 176 |
| 9 | 17 | SC |   |   | | 177 |
| 9 | 18 | EC |   |   | | 178 |
| 9 | 19 | NI |   |   | | 179 |
| 9 | 20 | TR |   |   | | 180 |
| 10 | 1 | ST |   |   | | 181 |
| 10 | 2 | VS |   |   | | 182 |
| 10 | 3 | CH |   |   | | 183 |
| 10 | 4 | LZ |   |   | | 184 |
| 10 | 5 | EM |   |   | | 185 |
| 10 | 6 | CA |   |   | | 186 |
| 10 | 7 | GE |   |   | | 187 |
| 10 | 8 | LI |   |   | | 188 |
| 10 | 9 | HF |   |   | | 189 |
| 10 | 10 | HB |   |   | | 190 |
| 10 | 11 | BV |   |   | | 191 |
| 10 | 12 | PE |   |   | | 192 |
| 10 | 13 | KK |   |   | | 193 |
| 10 | 14 | PG |   |   | | 194 |
| 10 | 15 | WL |   |   | Craig Paquette | 195 |
| 10 | 16 | DM |   |   | | 196 |
| 10 | 17 | SC |   |   | | 197 |
| 10 | 18 | EC |   |   | | 198 |
| 10 | 19 | NI |   |   | | 199 |
| 10 | 20 | TR |   |   | | 200 |
| 11 | 1 | ST |   |   | | 201 |
| 11 | 2 | VS |   |   | | 202 |
| 11 | 3 | CH |   |   | | 203 |
| 11 | 4 | LZ |   |   | | 204 |
| 11 | 5 | EM |   |   | | 205 |
| 11 | 6 | CA |   |   | | 206 |
| 11 | 7 | GE |   |   | | 207 |
| 11 | 8 | LI |   |   | | 208 |
| 11 | 9 | HF |   |   | | 209 |
| 11 | 10 | HB |   |   | | 210 |
| 11 | 11 | BV |   |   | | 211 |
| 11 | 12 | PE |   |   | | 212 |
| 11 | 13 | KK |   |   | | 213 |
| 11 | 14 | PG |   |   | John Halama, released Curtis Leskanic | 214 |
| 11 | 15 | WL |   |   | | 215 |
| 11 | 16 | DM |   |   | | 216 |
| 11 | 17 | SC |   |   | | 217 |
| 11 | 18 | EC |   |   | | 218 |
| 11 | 19 | NI |   |   | | 219 |
| 11 | 20 | TR |   |   | | 220 |