| Pick | Team | Player | Position | School | HT | WT |
|---|---|---|---|---|---|---|
| Justin Upton | OF | Great Bridge High School | - |
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| Alex Gordon | 3rd | Nebraska | - |
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| Jeff Clement | C | USC | - |
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| Ryan Zimmerman | 3rd | Virginia | - |
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| Ryan Braun | 3rd | Miami | - |
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| Ricky Romero | LHP | Cal State Fullerton | - |
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| Troy Tulowitzki | SS | Long Beach State | - |
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| Wade Townsend | RHP | Rice | - |
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| Mike Pelfrey | RHP | Wichita State | - |
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| Cameron Maybin | OF | T. C. Roberson High School | - |
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| Andrew McCutchen | OF | Ft. Meade Jr. Sr. High School | - |
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| Jay Bruce | OF | West Brook High School | - |
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| Brandon Snyder | C | Westfield High School | - |
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| Trevor Crowe | OF | Arizona | - |
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| Lance Broadway | RHP | TCU | - |
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| Chris Volstad | RHP | Palm Beach Gardens High School | - |
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| C.J. Henry | SS | Kansas | - |
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| Cesar Carrillo | RHP | Miami | - |
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| Mark Mayberry Jr. | LHP | Stanford | - |
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| Mark Pawelek | LHP | Springville High School | - |
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| Cliff Pennington | SS | Texas A&M | - |
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| Aaron Thompson | LHP | Second Baptist School | - |
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| Jacoby Ellsbury | OF | Oregon State | - |
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| Brian Bogusevic | LHP | Tulane | - |
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| Matt Garza | RHP | Fresno State | - |
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| Craig Hansen | RHP | St. John's | - |
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| Joey Devine | RHP | NC State | - |
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| Colby Rasmus | OF | Russell County High School | - |
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| Jacob Marceaux | RHP | McNeese State | - |
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| Tyler Greene | SS | Georgia Tech | - |
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| Matthew Torra | RHP | UMass | - |
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| Chaz Roe | RHP | Fayette Co Public Schools | - |
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| John Drennen | OF | Rancho Bernardo High School | - |
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| Ryan Tucker | RHP | Temple City High School | - |
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| Cesar Ramos | LHP | Long Beach State | - |
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| Travis Buck | OF | Arizona State | - |
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| Trevor Bell | RHP | Crescenta Valley High School | - |
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| Eli Iorg | OF | Tennessee | - |
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| Henry Sanchez | 1B | Mission Bay High School | - |
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| Luke Hochevar | RHP | Tennessee | - |
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| Beau Jones | LHP | Destrehan High School | - |
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| Clay Buchholz | RHP | United States | - |
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| Mark McCormick | RHP | Baylor | - |
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| Sean West | LHP | Captain Shreve High School | - |
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| Jed Lowrie | 2B | Stanford | - |
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| Tyler Herron | RHP | Wellington High School | - |
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| Michael Bowden | RHP | Waubonsie Valley High School | - |
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| Garrett Olson | LHP | Cal Poly | - |
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