| # | Team | Points | Top 5 Prospects |
| 1 | Boston | 218 | RF Daren Hamburg (2nd), SS Jhonny Peralta (6th), P Hide Hisahsi (8th), P Adam Loewen (17th), RF Dave Krynzel (22nd) |
| 2 | St. Louis | 117 | 2B James Guarino (10th), CF Freddie Lewis (13th), LF David Berrier (26th), C Tommy Arko (53rd), C Robert Escobar (65th) |
| 3 | Tampa Bay | 116 | RF Wes Bankston (9th), 2B Rudolf Dehaven (12th), CF Juan Ramirez (20th), RF Jonny Gomes (30th), |
| 4 | Houston | 103 | P Scott Kazmir (4th), P Eduardo Jusino (21st), C John Buck (25th), P Anthony Pluta (35th), P Kris Honel (85th) |
| 5 | Seattle | 81 | P Kurt Webb (7th), P Juan Done (28th), LF Rudy Guillen (31st), P Travis Blackley (88th), P Bobby Livingston (93rd) |
| 6 | Milwaukee | 74 | P Manny Parra (5th), SS J.J. Hardy (52nd), 2B Jose Raposa (58th), 1B Michael Johnson (66th), C Mitch Maier (81st) |
| 7 | San Diego | 71 | 2B Victor Diaz (19th), P Timothy Parkerson (33rd), C Brad Nelson (48th), LF Markus Marshburn (68th), P James Williams (76th) |
| 8 | Toronto | 70 | 1B Scott Byron (11th), RF David Murphy (23rd), SS Jose Castillo (37th), P Glen Olmstead (95th), |
| 9 | Anaheim | 57 | P Marc Cornell (24th), P Steven Shell (36th), 1B Casey Kotchman (49th), CF Alex Romero (64th), P Luke Hagerty (83rd) |
| 10 | Baltimore | 54 | P Beau Vaughan (1st), P John Maine (79th), |
| 11 | Minnesota | 51 | C Joe Mauer (32nd), RF James Stokes (38th), P Bobby Jenks (63rd), P Roosevelt Hudspeth (69th), C Jeff Mathis (73rd) |
| 12 | San Francisco | 51 | 3B Omar Quintanilla (3rd), 1B Josue Salo (98th), |
| 13 | New York (N) | 48 | C Richard Arms (14th), 1B Scott Thorman (42nd), SS Herbert Joslyn (87th), |
| 14 | Colorado | 43 | 1B Claude Slattery (27th), P Scott Baker (43rd), 3B Miguel Vega (51st), |
| 15 | Philadelphia | 39 | RF Jeremy Hermida (16th), RF Delmon Young (55th), 3B Matt Moses (84th), |
| 16 | Chicago (A) | 32 | RF Thomas Brice (15th), |
| 17 | Arizona | 27 | P Randy Mcgrane (18th), |
| 18 | Cincinnati | 26 | P Renato Alvarez (39th), P Jimmy Barthmaier (50th), 3B Edwin Encarnacion (97th), |
| 19 | Cleveland | 24 | P Francisco Cruceta (29th), RF Nicholas Armijo (75th), |
| 20 | Oakland | 22 | LF Brian Stavinsky (40th), P Raymond Schade (59th), |
| 21 | Montreal | 21 | P Jeff Allison (44th), CF Michael Bourn (54th), |
| 22 | Florida | 20 | P Jose Bazan (47th), 1B James Lesko (80th), 2B Rickie Weeks (82nd), |
| 23 | Detroit | 17 | LF Carlos Quentin (57th), LF Bernie Liriano (70th), P Andrew Miller (91st), SS Anderson Hernandez (99th), |
| 24 | Kansas City | 16 | C Robert Redick (56th), 1B Chad Santos (67th), |
| 25 | New York (A) | 15 | SS Kenneth Summerall (34th), |
| 26 | Atlanta | 13 | 2B Jon Schuerholz (41st), |
| 27 | Pittsburgh | 12 | P Leo Nunez (46th), |
| 28 | Los Angeles | 9 | P Perry Keifer (60th), 1B James Loney (96th), C Edwin Bellorin (100th), |
| 29 | Texas | 5 | 1B Vince Sinisi (74th), |
| 30 | Chicago (N) | 3 | 3B Alfredo Francisco (86th), |
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