| Major League Phase | |
| First Round | |
| 1. Nationals | Terrell Young, rhp, Reds |
| Skinny: Mississippi prep product always has had arm strength, but improved control and changeup in '08. | |
| 2. Mariners | Reegie Corona, ss/2b, Yankees |
| Skinny: Versatile middle infielder has defensive ability to stick; contact hitter has little power but runs well, walks. | |
| 3. Padres | Everth Cabrera, ss/2b, Rockies |
| Skinny: Squeezed off Rockies' full 40-man, Cabrera has plus speed and plays a fine shortstop but hasn't played above Sally League. | |
| 4. Pirates | Donald Veal, lhp, Cubs |
| Skinny: Once a top prospect, Veal had rough year but peaked at 94 mph with sink on fastball; mechanical issues leave control, breaking ball short. | |
| *5. Orioles | Lou Palmisano, c, Brewers |
| Skinny: Third-round pick out of JC in 2003, he missed most of 2008 with knee injury; had best offensive season in '07 at Double-A Huntsville. | |
| 6. Giants | Luis Perdomo, rhp, Cardinals |
| Skinny: Small-bodied righty has quick arm and fastball that reaches 94, complemented by short, sharp slider. | |
| 7. Braves | Pass |
| &8. Reds | David Patton, rhp, Rockies |
| Skinny: Aggressive with hard curveball in 82-85 mph range, tick-above-average fastball that has touched 94; 10.6 K/9 in Cal League. | |
| 9. Tigers | Kyle Bloom, lhp, Pirates |
| Skinny: Three-pitched 25-year-old, improved delivery led to velo jump (up to 92) late at Double-A; dominated in HWB. | |
| 10. Rockies | Pass |
| ^11. Royals | Jose Lugo, lhp, Twins |
| Skinny: Still learning control (and won't have command), but has plus-plus fastball with 91-95 mph velo, excellent sink. | |
| 12. Athletics | Ben Copeland, of, Giants |
| Skinny: Was Giants' top draft pick in 2005 (as fourth-rounder); solid tools and patience, hit tool is best asset, fourth OF profile. | |
| 13. Rangers | Pass |
| 14. Indians | Pass |
| 15. Diamondbacks | James Skelton, c, Tigers |
| Skinny: Lefthanded-hitting catcher with smallish frame, plus arm and good plate discipline who has career .416 OBP in minors. | |
| 16. Dodgers | Pass |
| 17. Marlins | Zack Kroenke, lhp, Yankees |
| Skinny: Lefty reliever has pie-throwing delivery that hinders command, but can run fastball up to 93 and has solid slider; more effective vs. RH hitters in '08. | |
| 18. Cardinals | Pass |
| 19. Blue Jays | Pass |
| 20. Astros | Gil de la Vara, lhp, Royals |
| Skinny: Teammate of Veal at Pima (Ariz.) JC; 87-89 mph fastball complements good curve and improved changeup. | |
| 21. Twins | Jason Jones, rhp, Yankees |
| Skinny: Big-bodied 26-year-old throws four pitches for strikes and competes; fringy fastball augmented by cutter, split-finger pitch. | |
| 22. White Sox | Pass |
| 23. Mets | Darren O'Day, rhp, Angels |
| Skinny: Sidearming former Florida closer sinks it, slides it; nondrafted free agent reached majors in '08, posted 4.57 ERA in 43.1 IP. | |
| 24. Yankees | Pass |
| 25. Brewers | Eduardo Morlan, rhp, Rays |
| Skinny: Former Twins farmhand struggled with Rays as velo fell; back up at high as 92 mph in Puerto Rican League this winter, showed 95 in the past. | |
| 26. Phillies | Bobby Mosebach, rhp, Angels |
| Skinny: Former Florida juco product uses sinker-slider combination to coax 2.04 groundout/airout ratio in Double-A Texas League; allowed just six home runs. | |
| 27. Red Sox | Miguel Gonzales, rhp, Angels |
| Skinny: Missed 2008 with injury, but thriving in Mexican Pacific League at 3-1, 0.99 this winter with 32-8 K-BB ratio in 35 IP. | |
| 28. Rays | Derek Rodriguez, rhp, White Sox |
| Skinny: Sidearming reliever uses fastball-split combo to handle lefthanded hitters (.648 OPS) as well as righties (.591). | |
| 29. Cubs | Pass |
| 30. Angels | Pass |
|
* Traded to Astros |
|
| Second Round | |
| 1. Padres | Ivan Nova, rhp, Yankees |
| Skinny: Tall 21-year-old has flashed three plus pitches at times but lacks consistency and deception; hit hard in FSL (.294 opponents average). | |
| 2. Mets | Rocky Cherry, rhp, Orioles |
| Skinny: Oklahoma product, 29, already has 48 innings of big league time; 6-foot-5 power righthander throws up to 95 mph with hard slider at his best. | |
| Triple-A Phase | |
| First Round | |
| 1. Nationals | Ricardo Nanita, of (White Sox) |
| 2. Mariners | Pat Ryan, rhp (Brewers) |
| 3. Padres | Pass |
| 4. Pirates | Andres Santos, lhp (Yankees) |
| 5. Orioles | Roberto Valido, ss (White Sox) |
| 6. Giants | Matt Yourkin, lhp (Marlins) |
| 7. Braves | Pass |
| 8. Reds | Francisco Lizarraga, ss (Dodgers) |
| 9. Tigers | Pass |
| 10. Rockies | Pass |
| 11. Royals | Luis Ortega, rhp (Nationals) |
| 12. Athletics | Yusef Carter, of (Cubs) |
| 13. Rangers | Elio Sarmiento, c (Giants) |
| 14. Indians | Pass |
| 15. Diamondbacks | Pass |
| 16. Dodgers | Anthony Hatch, 3b (Blue Jays) |
| 17. Marlins | Ryan Klosterman, ss (Blue Jays) |
| 18. Cardinals | Russell Haltiwanger, rhp (Royals) |
| 19. Blue Jays | Cody Haerther, 1b/of (Cardinals) |
| 20. Astros | Drew Locke, of/1b (Dodgers) |
| 21. Twins | Henry Arias, rhp (Reds) |
| 22. White Sox | Pass |
| 23. Mets | Carl Loadenthal, of (Braves) |
| 24. Yankees | Pass |
| 25. Brewers | Mark Holliman, rhp (Cubs) |
| 26. Phillies | Kyle Haines, 2b (Giants) |
| 27. Red Sox | Jason Rice, rhp (White Sox) |
| 28. Rays | Pass |
| 29. Cubs | Pass |
| 30. Angels | Pass |
| Second Round | |
| 4. Pirates | Rafael Quintero, if (Indians) |
| 5. Orioles | Josh Perrault, rhp (Nationals) |
| 11. Royals | John Suomi, c (Phillies) |
| 12. Athletics | Josue Selenes, rhp (Yankees) |
| 13. Rangers | Guider Rodriguez, ss (Brewers) |
| 17. Marlins | Brett Harker, rhp (Phillies) |
| 19. Blue Jays | David Shinskie, rhp (Twins) |
| 23. Mets | John Madden, rhp (Padres) |
| 25. Brewers | Jonny Ash, 2b (Astros) |
| 26. Phillies | Javis Diaz, of (Padres) |
| 27. Red Sox | Miguel Marquez, rhp (Mariners) |
| Third Round | |
| Pirates | Gerardo Esparza, rhp (Mariners) |
| Royals | Carlos Arias, rhp (Indians) |
| Marlins | Ron Hill, rhp (Phillies) |
| Brewers | Shane Justis, ss (Dodgers) |
| Fourth Round | |
| Brewers | Juan Sanchez, ss (Twins) |
| Double-A Phase | |
| Orioles | Andrew Barb, rhp, (Mariners) |