| Year | Rnd | Ovl | Phase | Player | Drafting Team | Pos | HiLvl | Played | Src | Drafted From | SF | State | AB | 2B | 3B | HR | RBI | SB | BAVG | W | L | ERA | SV | IP | SO | GS |
| 2006 | 1 | 4 | June-Reg | Brad Lincoln | Pittsburgh Pirates | P | MLB | 2004-2013 | C | University of Houston | SF | TX | 37 | 1 | 0 | 0 | 4 | 0 | .243 | 8 | 9 | 4.78 | 1 | 188 | 142 | 22 |
| 2006 | 2 | 48 | June-Reg | Mike Felix | Pittsburgh Pirates | P | A+ | 2004-2010 | C | Troy University | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 3 | 80 | June-Reg | Shelby Ford | Pittsburgh Pirates | 2B | AAA | 2004-2012 | C | Oklahoma State University | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 4 | 110 | June-Reg | Jared Hughes | Pittsburgh Pirates | P | MLB | 2004-2013 | C | Long Beach State University | SF | CA | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 2 | 3 | 3.01 | 2 | 87 | 60 | 0 |
| 2006 | 5 | 140 | June-Reg | Pat Bresnahan | Pittsburgh Pirates | P | AA | 2004-2012 | C | Arizona State University | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 6 | 170 | June-Reg | Jim Negrych | Pittsburgh Pirates | 2B | AAA | 2004-2013 | C | University of Pittsburgh | SF | PA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 7 | 200 | June-Reg | Austin McClune | Pittsburgh Pirates | CF | A+ | 2006-2010 | H | Edmond Santa Fe (Edmond,OK) | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 8 | 230 | June-Reg | Alex Presley | Pittsburgh Pirates | CF | MLB | 2004-2013 | C | University of Mississippi | SF | MS | 584 | 27 | 13 | 14 | 45 | 19 | .260 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 9 | 260 | June-Reg | Steve MacFarland | Pittsburgh Pirates | P | A | 2004-2011 | C | Lamar University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 10 | 290 | June-Reg | Charles Benoit | Pittsburgh Pirates | P | A+ | 2004-2008 | C | Oklahoma State University | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 11 | 320 | June-Reg | Lonnie Chisenhall ** | Pittsburgh Pirates | 3B | MLB | 2007-2013 | H | West Carteret (Morehead City,NC) | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 12 | 350 | June-Reg | Kent Sakamoto | Pittsburgh Pirates | 1B | A+ | 2003-2011 | C | Fresno State University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 13 | 380 | June-Reg | Brandon Holden | Pittsburgh Pirates | P | A | 2007-2010 | H | Douglas (Parkland,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 14 | 410 | June-Reg | Greg Smith | Pittsburgh Pirates | 1B | A- | 2003-2006 | C | Fordham University | SF | NY | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 15 | 440 | June-Reg | James Barksdale | Pittsburgh Pirates | CF | A+ | 2006-2008 | C | University of North Alabama | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 16 | 470 | June-Reg | Kris Watts | Pittsburgh Pirates | C | AAA | 2005-2013 | C | Santa Clara University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 17 | 500 | June-Reg | Michael Crotta | Pittsburgh Pirates | P | MLB | 2004-2013 | C | Florida Atlantic University | SF | FL | -- | -- | -- | -- | -- | -- | -- | 0 | 1 | 9.28 | 0 | 11 | 7 | 0 |
| 2006 | 18 | 530 | June-Reg | Francisco Ortiz | Pittsburgh Pirates | P | A | 2006-2010 | H | Puerto Rico Baseball Acad (Gurabo,PR) | SF | PR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 19 | 560 | June-Reg | Jason Moseby | Pittsburgh Pirates | CF | - | H | Newport (Bellevue,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 20 | 590 | June-Reg | Matt Clarkson | Pittsburgh Pirates | C | A- | 2005-2007 | C | Oklahoma State University | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 21 | 620 | June-Reg | Kody Paul | Pittsburgh Pirates | P | NCAA | 2007-2007 | H | Glynn Academy (Brunswick,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 22 | 650 | June-Reg | Miles Durham | Pittsburgh Pirates | RF | AAA | 2004-2012 | C | Northwestern State University | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 23 | 680 | June-Reg | Preston Claiborne ** | Pittsburgh Pirates | P | MLB | 2007-2013 | H | Smith (Carrollton,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 24 | 710 | June-Reg | Scott Massey | Pittsburgh Pirates | P | RK | 2003-2006 | C | University of Southern Mississippi | SF | MS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 25 | 740 | June-Reg | Adam Simon | Pittsburgh Pirates | P | A+ | 2003-2008 | C | San Diego State University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 26 | 770 | June-Reg | Ryan Kelly | Pittsburgh Pirates | P | AAA | 2007-2013 | H | Hilton Head (Hilton Head,SC) | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 27 | 800 | June-Reg | Cache Breedlove | Pittsburgh Pirates | 3B | - | H | Edmond Santa Fe (Edmond,OK) | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 28 | 830 | June-Reg | Rudy Owens | Pittsburgh Pirates | P | AAA | 2007-2013 | H | Mesa (Mesa,AZ) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 29 | 860 | June-Reg | Brandon Williams | Pittsburgh Pirates | P | AA | 2006-2008 | C | University of South Carolina-Upstate | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 30 | 890 | June-Reg | Alphonso Owens | Pittsburgh Pirates | CF | - | H | Dillon (Dillon,SC) | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 31 | 920 | June-Reg | Jared Keel | Pittsburgh Pirates | 3B | A+ | 2005-2010 | C | Troy University | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 32 | 950 | June-Reg | Jorge Charry | Pittsburgh Pirates | P | A | 2006-2009 | C | Lake City Community College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 33 | 980 | June-Reg | Victor Alvarez | Pittsburgh Pirates | SS | AA | 2006-2008 | C | Cumberland University | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 34 | 1010 | June-Reg | Pernell Halliman ** | Pittsburgh Pirates | P | RK | 2006-2009 | C | West Hills College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 35 | 1040 | June-Reg | Josue Peley | Pittsburgh Pirates | SS | AA | 2007-2012 | C | Seminole State College | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 36 | 1070 | June-Reg | Chad Arnold ** | Pittsburgh Pirates | P | NCAA | 2008-2011 | H | Southridge (Kennewick,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 37 | 1100 | June-Reg | Damian Walcott | Pittsburgh Pirates | CF | Ind | 2009-2009 | C | Brookdale Community College | SF | NJ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 38 | 1130 | June-Reg | Matthew McCullen | Pittsburgh Pirates | P | RK | 2006-2007 | C | Western Carolina University | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 39 | 1160 | June-Reg | Tom Hagan | Pittsburgh Pirates | LF | A | 2003-2008 | C | University of Virginia | SF | VA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 40 | 1190 | June-Reg | Philip Brannon | Pittsburgh Pirates | P | NCAA | 2009-2011 | H | Broome (Spartanburg,SC) | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 41 | 1220 | June-Reg | Scott Kuhns | Pittsburgh Pirates | P | - | C | Parkland College | SF | IL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 42 | 1250 | June-Reg | Jonathan Harmston | Pittsburgh Pirates | P | NCAA | 2007-2009 | H | Bullard (Fresno,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 43 | 1279 | June-Reg | Devin Copley | Pittsburgh Pirates | P | RK | 2007-2007 | C | Florida Gulf Coast University | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 44 | 1308 | June-Reg | Douglas Hines | Pittsburgh Pirates | SS | - | H | Hudson (Lufkin,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 45 | 1337 | June-Reg | Paul-Michael Klingsberg ** | Pittsburgh Pirates | 1B | RK | 2007-2009 | H | Notre Dame (Sherman Oaks,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 46 | 1366 | June-Reg | Ryan Groth ** | Pittsburgh Pirates | RF | A | 2006-2009 | C | Indian River State College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 47 | 1394 | June-Reg | Brandon Wilkerson | Pittsburgh Pirates | SS | RK | 2008-2012 | H | Lamar (Arlington,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 48 | 1422 | June-Reg | Ken Wieda | Pittsburgh Pirates | P | - | C | Vernon College | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 49 | 1450 | June-Reg | Carson Middleton | Pittsburgh Pirates | P | NCAA | 2008-2008 | H | Lindale (Lindale,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 50 | 1478 | June-Reg | Marquise Zachery | Pittsburgh Pirates | CF | - | C | Lake City Community College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |