| 1 | 4 | June-Reg | Gavin Floyd | P | 18 | 6-5 | 210 | R | R | MLB | 2004-2009 | Mount St. Joseph (Severna Park,MD) | $4,200,000 |
| 4 | 110 | June-Reg | Terry Jones | IF | 18 | 6-2 | 190 | R | R | A+ | | Upland (Upland,CA) | $500,000 |
| 5 | 140 | June-Reg | Ryan Howard | 1B | 21 | 6-4 | 230 | L | L | MLB | 2004-2009 | Missouri State University | $230,000 |
| 6 | 170 | June-Reg | Bryan Hansen | 1B | 18 | 6-2 | 205 | L | L | AA | | Longwood (Middle Island,NY) | $150,000 |
| 7 | 200 | June-Reg | Vinnie DeChristofaro | P | 19 | 6-1 | 170 | L | L | A | | Richmond Hill (Richmond Hill,GA) | $129,000 |
| 8 | 230 | June-Reg | Taft Cable | P | 20 | 6-2 | 210 | R | R | AA | | University of North Carolina-Greensboro | $95,000 |
| 9 | 260 | June-Reg | Chris Roberson | OF | 21 | 6-2 | 175 | R | R | MLB | 2006-2007 | Feather River College | $55,000 |
| 10 | 290** | June-Reg | Rocky Cherry | P | 21 | 6-5 | 210 | R | R | MLB | 2007-2008 | University of Oklahoma | |
| 11 | 320 | June-Reg | Matt Sweeney | P | 18 | 6-2 | 180 | R | R | AA | | Steinert (Trenton,NJ) | |
| 12 | 350 | June-Reg | Rod Perry | OF | 22 | 5-10 | 195 | R | R | A+ | | Penn State University | |
| 13 | 380 | June-Reg | Andre Marshall | OF | 20 | 6-5 | 205 | B | R | A | | University of Washington | |
| 14 | 410 | June-Reg | Mario Delgado | IF | 21 | 6-0 | 220 | L | L | AA | | Oklahoma City University | |
| 15 | 440 | June-Reg | Tim Davis | P | 22 | 6-4 | 230 | L | L | A | | University of South Alabama | |
| 16 | 470 | June-Reg | Ben Margalski | C | 21 | 6-2 | 210 | L | R | A+ | | Missouri State University | |
| 17 | 500 | June-Reg | Ryan Hutchison | P | 22 | 6-0 | 205 | R | R | AAA | | Western Kentucky University | |
| 18 | 530 | June-Reg | Ben Ally | P | 22 | 6-2 | 205 | R | R | A- | | Warner Southern College | |
| 19 | 560 | June-Reg | Matt Squires | P | 22 | 5-10 | 200 | L | L | AA | | Whitworth University | |
| 20 | 590 | June-Reg | Vince Vukovich | OF | 21 | 6-0 | 175 | L | R | A+ | | University of Delaware | |
| 21 | 620** | June-Reg | Julian Williams | CF | 17 | 5-11 | 175 | R | R | A | | Upland (Upland,CA) | |
| 22 | 650 | June-Reg | Michael Floyd | | 21 | 6-3 | 185 | R | R | A+ | | University of South Carolina | |
| 23 | 680 | June-Reg | Joshua Cisneros | C | 21 | 5-10 | 190 | R | R | Ind | | West Virginia University | |
| 24 | 710 | June-Reg | Kris Lammers | | 22 | 6-2 | 195 | L | L | Rookie | | Middle Tennessee State University | |
| 25 | 740 | June-Reg | Josh Scott | P | 21 | 6-3 | 190 | L | L | A | | Baylor University | |
| 26 | 770 | June-Reg | Layne Dawson | P | 21 | 6-2 | 180 | R | R | AA | | University of Memphis | |
| 27 | 800 | June-Reg | Jay Bernard | P | 22 | 6-5 | 220 | R | R | A | | Troy University | |
| 28 | 830 | June-Reg | Michael Nall | | 22 | 6-1 | 190 | R | R | A- | | Northwestern University | |
| 29 | 860 | June-Reg | Jeremy Kurella | | 22 | 6-1 | 190 | B | R | College | | University of Central Florida | |
| 30 | 890 | June-Reg | Kris Bennett | 3B | 21 | 5-10 | 170 | R | R | A+ | | University of Tennessee | |
| 31 | 920 | June-Reg | Gabrial Johnston | C | | | 0 | | | - | | Sonoma State University | |
| 32 | 950 | June-Reg | Josh Miller | P | 22 | 6-1 | 200 | R | R | AAA | | North Carolina State University | |
| 33 | 980 | June-Reg | Daniel McCall | P | 22 | 6-0 | 175 | L | L | Ind | | Penn State University | |
| 34 | 1010 | June-Reg | Brian Schriner | | 22 | 6-3 | 215 | R | R | Rookie | | University of Louisiana-Monroe | |
| 35 | 1040 | June-Reg | Nick Glaser | P | 22 | 6-2 | 190 | R | R | A- | | Clemson University | |
| 36 | 1070 | June-Reg | Jeff Phelps | IF | 22 | 6-0 | 195 | R | R | AA | | Arizona State University | |
| 37 | 1100 | June-Reg | Wes Carroll | 2B | 22 | 5-11 | 185 | R | R | AAA | - | University of Evansville | |
| 38 | 1130 | June-Reg | Jaime Martinez | | | | | | | Ind | | Hueneme (Oxnard,CA) | |
| 39 | 1160** | June-Reg | Jason Jaramillo | | 18 | 6-0 | 200 | B | R | MLB | 2009-2009 | Case (Racine,WI) | |
| 40 | 1190** | June-Reg | Arnold Hughey | | 18 | 6-2 | 215 | L | L | A- | | Venice (Venice,FL) | |
| 41 | 1219 | June-Reg | Dustin Miller | P | | | | | | Rookie | | Diamond Bar (Diamond Bar,CA) | |
| 42 | 1248** | June-Reg | Will Thompson | | 18 | 6-1 | 180 | L | L | AAA | | Loyola-Sacred Heart (Missoula,MT) | |
| 43 | 1276** | June-Reg | Andy Lytle | | 18 | 6-1 | 165 | R | R | A | | Highlands Ranch (Highlands Ranch,CO) | |
| 44 | 1304 | June-Reg | Humberto Gonzales | SS-2B | 20 | 5-10 | 155 | R | R | - | | Rainier Beach (Seattle,WA) | |
| 45 | 1332 | June-Reg | Jared Birrenkott | C | 18 | 6-3 | 205 | L | R | College | | Granite Hills (El Cajon,CA) | |
| 46 | 1360 | June-Reg | Allen Hicks | OF | | | 0 | | | - | | King (Tampa,FL) | |
| 47 | 1388 | June-Reg | Sean Walsh | 3B | 21 | 6-4 | 220 | R | R | AA | - | North Carolina State University | |
| 48 | 1415 | June-Reg | Maximo Reyes | P | 19 | 5-9 | 170 | R | R | AAA | | St. Petersburg College | |