| Pick | Sess | Round | RdPk | Team | pick |
| 1 | p | 13 | 1 | Camano Island | Felix Hernandez |
| 2 | p | 13 | 2 | Detroit | Matt Cain |
| 3 | p | 13 | 3 | Duluth | Huston Street |
| 4 | p | 13 | 4 | Washington | Brian McCann |
| 5 | p | 13 | 5 | Scottsdale | Zach Duke |
| 6 | p | 13 | 6 | Seoul | Mark Ellis |
| 7 | p | 13 | 7 | Rosehaven | Daniel Cabrera |
| 8 | p | 13 | 8 | Texas | Jeff Francoeur |
| 9 | p | 13 | 9 | Camano Island | Jeremy Hermida |
| 10 | p | 13 | 10 | Hollywood | Chad Tracy |
| 11 | p | 13 | 11 | Santa Clara | Felipe Lopez |
| 12 | p | 13 | 12 | Madiba | Francisco Liriano |
| 13 | p | 13 | 13 | New Jersey | Chad Cordero |
| 14 | p | 13 | 14 | Tampa Bay | Paul Maholm |
| 15 | p | 13 | 15 | Charlotte | Ervin Santana |
| 16 | p | 13 | 16 | New Orleans | Ryan Zimmerman |
| 17 | p | 13 | 17 | Seoul | Dioner Navarro |
| 18 | p | 13 | 18 | Carolina | Jermaine Dye |
| 19 | p | 13 | 19 | Seoul | Johnny Gomes |
| 20 | p | 13 | 20 | Washington | Josh Towers |
| 21 | p | 13 | 21 | Madiba | Justin Verlander |
| 22 | p | 13 | 22 | Jamaica | Prince Fielder |
| 23 | p | 13 | 23 | Bellingham | Bill Hall |
| 24 | p | 13 | 24 | Mystic | Derrick Turnbow |
| 25 | p | 13 | 25 | Dresden | Brandon McCarthy |
| 26 | p | 13 | 26 | Madiba | Anthony Reyes |
| 27 | p | 14 | 1 | Carolina | Robinson Cano |
| 28 | p | 14 | 2 | Santa Clara | J.J. Hardy |
| 29 | p | 14 | 3 | Charlotte | Matt Holliday |
| 30 | p | 14 | 4 | New Orleans | Andy Marte |
| 31 | p | 14 | 5 | New Jersey | Yadier Molina |
| 32 | p | 14 | 6 | Nashua | Jonathan Papelbon |
| 33 | p | 14 | 7 | Rosehaven | Chris Shelton |
| 34 | p | 14 | 8 | Scottsdale | Tony Clark |
| 35 | p | 14 | 9 | Washington | Scott Baker |
| 36 | p | 14 | 10 | Duluth | Brandon Claussen |
| 37 | LD | 14 | 11 | Jamaica | Kyle Davies |
| 38 | LD | 14 | 12 | Kiev | Jason Johnson |
| 39 | LD | 14 | 13 | Nashua | Jason Vargas |
| 40 | LD | 15 | 1 | Carolina | Jason LaRue |
| 41 | LD | 15 | 2 | Santa Clara | Aaron Heilman |
| 42 | LD | 15 | 3 | Charlotte | Wily Taveras |
| 43 | LD | 15 | 4 | Tampa Bay | Jay Gibbons |
| 44 | LD | 15 | 5 | New Orleans | Conor Jackson |
| 45 | LD | 15 | 6 | New Jersey | Kirk Saarloos |
| 46 | LD | 15 | 7 | Jamaica | Ryan Dempster |
| 47 | LD | 15 | 8 | Texas | Bobby Jenks |
| 48 | LD | 15 | 9 | Santa Clara | Josh Willingham |
| 49 | LD | 15 | 10 | Rosehaven | Emil Brown |
| 50 | LD | 15 | 11 | Bellingham | Tadahiro Iguchi |
| 51 | LD | 15 | 12 | Scottsdale | Garrett Atkins |
| 52 | LD | 15 | 13 | Washington | Aaron Hill |
| 53 | LD | 15 | 14 | Duluth | Curtis Granderson |
| 54 | LD | 15 | 15 | Hollywood | Bobby Howry |
| 55 | LD | 15 | 16 | Maui | Tomo Ohka |
| 56 | LD | 15 | 17 | Kiev | Bill Mueller |
| 57 | LD | 15 | 18 | Nashua | Jose Valverde |
| 58 | LD | 16 | 1 | Carolina | Wilson Betemit |
| 59 | LD | 16 | 2 | Cincinnati | Mike Jacobs |
| 60 | LD | 16 | 3 | Charlotte | Victor Zambrano |
| 61 | LD | 16 | 4 | Tampa Bay | Freddy Sanchez |
| 62 | LD | 16 | 5 | New Orleans | Casey Fossum |
| 63 | LD | 16 | 6 | New Jersey | Chien-Ming Wang |
| 64 | LD | 16 | 7 | Jamaica | Jason Jennings |
| 65 | LD | 16 | 8 | Dresden | Neil Cotts |
| 66 | LD | 16 | 9 | Santa Clara | Ryan Langerhans |
| 67 | LD | 16 | 10 | Rosehaven | Kyle Lohse |
| 68 | LD | 16 | 11 | Camano Island | Todd Jones |
| 69 | LD | 16 | 12 | Rosehaven | Juan Encarnacion |
| 70 | LD | 16 | 13 | Bellingham | Cory Lidle |
| 71 | LD | 16 | 14 | Scottsdale | Craig Counsell |
| 72 | LD | 16 | 15 | Washington | Scott Elarton |
| 73 | LD | 16 | 16 | Duluth | Dan Johnson |
| 74 | LD | 16 | 17 | Hollywood | Kyle Farnsworth |
| 75 | LD | 16 | 18 | Maui | Jae Seo |
| 76 | LD | 16 | 19 | Kiev | Hector Carrasco |
| 77 | LD | 16 | 20 | Nashua | Edwin Encarnacion |
| 78 | LD | 17 | 1 | Carolina | Robinson Tejada |
| 79 | LD | 17 | 2 | Hollywood | Tom Gordon |
| 80 | LD | 17 | 3 | Charlotte | Mark Grudzielanek |
| 81 | LD | 17 | 4 | Tampa Bay | Jesse Crain |
| 82 | LD | 17 | 5 | New Orleans | Ryan Madson |
| 83 | LD | 17 | 6 | Mystic | Jason Phillips |
| 84 | LD | 17 | 7 | Jamaica | Magglio Ordonez |
| 85 | LD | 17 | 8 | Texas | Yuniesky Betancourt |
| 86 | LD | 17 | 9 | Santa Clara | Scott Olsen |
| 87 | LD | 17 | 10 | Camano Island | Dan Wheeler |
| 88 | LD | 17 | 11 | Detroit | Cliff Politte |
| 89 | LD | 17 | 12 | Rosehaven | Rich Aurilia |
| 90 | LD | 17 | 13 | Bellingham | Brian Fuentes |
| 91 | LD | 17 | 14 | Scottsdale | Al Reyes |
| 92 | LD | 17 | 15 | Washington | Kenny Lofton |
| 93 | LD | 17 | 16 | Duluth | Chris Burke |
| 94 | LD | 17 | 17 | Cambridge | Mike Timlin |
| 95 | LD | 17 | 18 | Hollywood | Joaquin Benoit |
| 96 | LD | 17 | 19 | Maui | Rondell White |
| 97 | LD | 17 | 20 | Kiev | Damian Miller |
| 98 | LD | 17 | 21 | Nashua | Fernando Cabrera |
| 99 | LD | 18 | 1 | Carolina | Casey Blake |
| 100 | LD | 18 | 2 | Cincinnati | Ben Broussard |
| 101 | LD | 18 | 3 | Charlotte | Aaron Fultz |
| 102 | LD | 18 | 4 | Tampa Bay | Dmitri Young |
| 103 | LD | 18 | 5 | New Orleans | Salomon Torres |
| 104 | LD | 18 | 6 | New Jersey | Javier Valentine |
| 105 | LD | 18 | 7 | Jamaica | Andy Sisco |
| 106 | LD | 18 | 8 | Texas | Scott Eyre |
| 107 | LD | 18 | 9 | Santa Clara | Scott Downs |
| 108 | LD | 18 | 10 | Detroit | Mike Gonzalez |
| 109 | LD | 18 | 11 | Camano Island | Luis Ayala |
| 110 | LD | 18 | 12 | Rosehaven | Brian Moehler |
| 111 | LD | 18 | 13 | Bellingham | Bob Wickman |
| 112 | LD | 18 | 14 | Hollywood | David Riske |
| 113 | LD | 18 | 15 | Washington | Clay Hensley |
| 114 | LD | 18 | 16 | Duluth | Juan Dominguez |
| 115 | LD | 18 | 17 | Cambridge | Will Ohman |
| 116 | LD | 18 | 18 | Hollywood | Ugueth urbina |
| 117 | LD | 18 | 19 | Maui | Victor Santos |
| 118 | LD | 18 | 20 | Kiev | Matt Stairs |
| 119 | LD | 18 | 21 | Nashua | Ryan Church |
| 120 | LD | 19 | 1 | Carolina | Justin Speier |
| 121 | LD | 19 | 2 | Nashua | Todd Walker |
| 122 | LD | 19 | 3 | Charlotte | Michael Wuertz |
| 123 | LD | 19 | 4 | Tampa Bay | Kameron Loe |
| 124 | LD | 19 | 5 | New Orleans | Alex S. Gonzalez |
| 125 | LD | 19 | 6 | New Jersey | Travis Lee |
| 126 | LD | 19 | 7 | Jamaica | Mike Matheny |
| 127 | LD | 19 | 8 | Texas | Aaron Small |
| 128 | LD | 19 | 9 | Santa Clara | Mark Sweeney |
| 129 | LD | 19 | 10 | Camano Island | Arthur Rhodes |
| 130 | LD | 19 | 11 | Detroit | Shawn Estes |
| 131 | LD | 19 | 12 | Rosehaven | Julio Mateo |
| 132 | LD | 19 | 13 | Bellingham | Kent Mercker |
| 133 | LD | 19 | 14 | Scottsdale | Craig Monroe |
| 134 | LD | 19 | 15 | Washington | Chris Spurling |
| 135 | LD | 19 | 16 | Duluth | Tony Graffanino |
| 136 | LD | 19 | 17 | Cambridge | Antonio Perez |
| 137 | LD | 19 | 18 | Hollywood | Jose Cruz |
| 138 | LD | 19 | 19 | Maui | Aaron Cook |
| 139 | LD | 19 | 20 | Kiev | Gary Matthews |
| 140 | LD | 19 | 21 | Nashua | Matt Murton |
| 141 | LD | 20 | 1 | Carolina | Rudy Seanez |
| 142 | LD | 20 | 2 | Washington | Mike Cameron |
| 143 | LD | 20 | 3 | Charlotte | Lance Niekro |
| 144 | LD | 20 | 4 | Tampa Bay | Josh Fogg |
| 145 | LD | 20 | 5 | New Orleans | Chad Qualls |
| 146 | LD | 20 | 6 | New Jersey | Todd Williams |
| 147 | LD | 20 | 7 | Jamaica | Mike MacDougal |
| 148 | LD | 20 | 8 | Texas | Mark Teahen |
| 149 | LD | 20 | 9 | Santa Clara | Jason Michaels |
| 150 | LD | 20 | 10 | Cambridge | Rick Helling |
| 151 | LD | 20 | 11 | Swanee River | Neifi Perez |
| 152 | LD | 20 | 12 | Rosehaven | Jason Frasor |
| 153 | LD | 20 | 13 | Dresden | Ryan Doumit |
| 154 | LD | 20 | 14 | Scottsdale | Roberto Hernandez |
| 155 | LD | 20 | 15 | Washington | Shigetoshi Hasegawa |
| 156 | LD | 20 | 16 | Duluth | Chuck James |
| 157 | LD | 20 | 17 | New Jersey | So Taguchi |
| 158 | LD | 20 | 18 | Swanee River | Abraham O. Nunez |
| 159 | LD | 20 | 19 | Seoul | Brad Thompson |
| 160 | LD | 20 | 20 | Madiba | Matthew LeCroy |
| 161 | LD | 20 | 21 | Texas | Brandon Donnelly |
| 162 | LD | 20 | 22 | Seoul | Scott Schoeneweiss |
| 163 | LD | 20 | 23 | Seoul | Chris Reitsma |
| 164 | LD | 20 | 24 | Mystic | Gary Majewski |
| 165 | LD | 20 | 25 | Kiev | Jay Payton |
| 166 | LD | 20 | 26 | Nashua | Hayden Penn |
| 167 | LD | 21 | 1 | Carolina | Jason Ellison |
| 168 | LD | 21 | 2 | Cincinnati | John Wasdin |
| 169 | LD | 21 | 3 | Charlotte | Runelvys Hernandez |
| 170 | LD | 21 | 4 | Tampa Bay | Dave Roberts |
| 171 | LD | 21 | 5 | New Orleans | Mike Morse |
| 172 | LD | 21 | 6 | New Jersey | Byung Hung Kim |
| 173 | LD | 21 | 7 | Jamaica | Russ Springer |
| 174 | LD | 21 | 8 | Texas | Franklyn German |
| 175 | LD | 21 | 9 | Santa Clara | D.J. Carrasco |
| 176 | LD | 21 | 10 | Camano Island | Brad Ausmus |
| 177 | LD | 21 | 11 | Detroit | Luis A. Gonzalez |
| 178 | LD | 21 | 12 | Rosehaven | Pete Walker |
| 179 | LD | 21 | 13 | Bellingham | Duaner Sanchez |
| 180 | LD | 21 | 14 | Scottsdale | Aknori Otsuka |
| 181 | LD | 21 | 15 | Washington | Brian N. Anderson |
| 182 | LD | 21 | 16 | Duluth | Chris Ray |
| 183 | LD | 21 | 17 | Cambridge | Robert Fick |
| 184 | LD | 21 | 18 | Swanee River | Jay Witasick |
| 185 | LD | 21 | 19 | Nashua | Chad Orvella |
| 186 | LD | 21 | 20 | Madiba | Craig Hansen |
| 187 | LD | 21 | 21 | Dresden | Frank Catalanotto |
| 188 | LD | 21 | 22 | Hollywood | Alex Sanchez |
| 189 | LD | 21 | 23 | Maui | Elmer Dessens |
| 190 | LD | 21 | 24 | Mystic | Ricky Ledee |
| 191 | LD | 21 | 25 | Kiev | Adam Kennedy |
| 192 | LD | 21 | 26 | Carolina | Humberto Cota |
| 193 | LD | 22 | 1 | Carolina | Juan Rivera |
| 194 | A | 22 | 2 | Dresden | Matt Guerrier |
| 195 | A | 22 | 3 | Charlotte | Ramon Castro |
| 196 | A | 22 | 4 | Tampa Bay | David Weathers |
| 197 | A | 22 | 5 | New Orleans | Kelly Johnson |
| 198 | A | 22 | 6 | New Jersey | Giovanni Carrera |
| 199 | A | 22 | 7 | Jamaica | Jerry Hairston |
| 200 | A | 22 | 8 | Texas | Pete Orr |
| 201 | A | 22 | 9 | Santa Clara | Jeff Fassero |
| 202 | A | 22 | 10 | Detroit | Dustin McGowan |
| 203 | A | 22 | 11 | Camano Island | Dustin Mohr |
| 204 | A | 22 | 12 | Rosehaven | Julio Franco |
| 205 | A | 22 | 13 | Cambridge | Jamie Walker |
| 206 | A | 22 | 14 | Scottsdale | Ron Villone |
| 207 | A | 22 | 15 | Washington | Mike Redmond |
| 208 | A | 22 | 16 | Duluth | Jose Molina |
| 209 | A | 22 | 17 | Cambridge | John Foster |
| 210 | A | 22 | 18 | Swanee River | Juan Padilla |
| 211 | A | 22 | 19 | Nashua | Amborix Burgos |
| 212 | A | 22 | 20 | Washington | Todd Pratt |
| 213 | A | 22 | 21 | Dresden | Ryan Shealy |
| 214 | A | 22 | 22 | Hollywood | Alex Gonzalez |
| 215 | A | 22 | 23 | Cincinnati | Chris Gomez |
| 216 | A | 22 | 24 | Mystic | Julian Tavarez |
| 217 | A | 22 | 25 | Kiev | Vinnie Chulk |
| 218 | A | 22 | 26 | Washington | Wes Helms |
| 219 | A | 23 | 1 | Carolina | John Grabow |
| 220 | A | 23 | 2 | Cincinnati | Joe Borkowski |
| 221 | A | 23 | 3 | Charlotte | Julio Santana |