| 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 | 2 | 62 | June-Reg | Kevin Mulvey | New York Mets | P | MLB | 2004-2012 | C | Villanova University | SF | PA | 7 | 0 | 0 | 0 | 0 | 0 | .143 | 0 | 3 | 7.90 | 0 | 27 | 19 | 4 |
| 2006 | 3 | 94 | June-Reg | Joe Smith | New York Mets | P | MLB | 2004-2013 | C | Wright State University | SF | OH | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 21 | 14 | 3.11 | 0 | 316 | 257 | 0 |
| 2006 | 4 | 124 | June-Reg | John Holdzkom | New York Mets | P | A+ | 2006-2012 | C | Salt Lake Community College | SF | UT | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 5 | 154 | June-Reg | Steve Holmes | New York Mets | P | NCAA | 2004-2006 | C | University of Rhode Island | SF | RI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 6 | 184 | June-Reg | Scott Schafer | New York Mets | P | RK | 2006-2006 | H | Pasadena Memorial (Pasadena,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 7 | 214 | June-Reg | Daniel Stegall | New York Mets | OF | A+ | 2006-2009 | H | Greenwood (Greenwood,AR) | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 8 | 244 | June-Reg | Nathan Hedrick | New York Mets | P | RK | 2006-2007 | C | Barton County Community College | SF | KS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 9 | 274 | June-Reg | Jeremy Barfield ** | New York Mets | OF | AA | 2008-2013 | H | Klein (Klein,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 10 | 304 | June-Reg | Phillips Orta | New York Mets | P | A | 2007-2009 | C | Western Nebraska Community College | SF | NE | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 11 | 334 | June-Reg | Andy Moye ** | New York Mets | P | AA | 2008-2013 | H | Alpharetta (Alpharetta,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 12 | 364 | June-Reg | Nick Giarraputo | New York Mets | 3B | A | 2006-2012 | H | Simi Valley (Simi Valley,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 13 | 394 | June-Reg | Daniel Murphy | New York Mets | 3B | MLB | 2004-2012 | C | Jacksonville University | SF | FL | 1601 | 115 | 12 | 26 | 194 | 19 | .292 | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 14 | 424 | June-Reg | Todd Privett | New York Mets | P | A | 2006-2012 | C | College of Southern Idaho | SF | ID | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 15 | 454 | June-Reg | Justin Dalles ** | New York Mets | C | A+ | 2008-2012 | H | Park Vista (Boynton Beach,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 16 | 484 | June-Reg | Tobi Stoner | New York Mets | P | MLB | 2005-2012 | C | Davis and Elkins College | SF | WV | -- | -- | -- | -- | -- | -- | -- | 0 | 1 | 3.97 | 0 | 11 | 5 | 0 |
| 2006 | 17 | 514 | June-Reg | Stephen Puhl | New York Mets | C | A | 2006-2008 | C | St. Edward's University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 18 | 544 | June-Reg | Ritchie Price | New York Mets | SS | A- | 2003-2006 | C | University of Kansas | SF | KS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 19 | 574 | June-Reg | Justin Woodall ** | New York Mets | P | A | 2011-2012 | H | Lafayette (Ellisville,MS) | SF | MS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 20 | 604 | June-Reg | Jason Jacobs | New York Mets | C | A+ | 2003-2009 | C | University of Georgia | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 21 | 634 | June-Reg | Joel Wells | New York Mets | 1B | - | C | Abilene Christian University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 22 | 664 | June-Reg | Timothy Stronach | New York Mets | P | A+ | 2006-2011 | C | Worcester State College | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 23 | 694 | June-Reg | Nicholas Waechter | New York Mets | P | A+ | 2006-2009 | C | Western Oregon University | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 24 | 724 | June-Reg | Valentin Ramos | New York Mets | 1B | RK | 2006-2008 | H | Sallisaw (Sallisaw,OK) | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 25 | 754 | June-Reg | Steven Cheney | New York Mets | P | A+ | 2006-2008 | C | Florida Gulf Coast University | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 26 | 784 | June-Reg | Dustin Martin | New York Mets | OF | AAA | 2003-2012 | C | Sam Houston State University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 27 | 814 | June-Reg | Tim Haines | New York Mets | P | A- | 2005-2012 | C | University of Texas-Pan American | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 28 | 844 | June-Reg | Will Bashelor | New York Mets | OF | A- | 2004-2006 | C | Dartmouth College | SF | NH | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 29 | 874 | June-Reg | Jake Eigsti | New York Mets | SS | AA | 2003-2012 | C | Indiana State University | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 30 | 904 | June-Reg | Ricky Sparks | New York Mets | P | A | 2006-2007 | C | Dallas Baptist University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 31 | 934 | June-Reg | Jeremy Hambrice | New York Mets | OF | A- | 2006-2007 | C | Southern Arkansas University | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 32 | 964 | June-Reg | B.J. Roper-Hubbert | New York Mets | C | - | C | Alcorn State University | SF | MS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 2006 | 33 | 994 | June-Reg | Teddy Dziuba | New York Mets | C | AA | 2006-2007 | C | Babson College | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 34 | 1024 | June-Reg | J.R. Voyles | New York Mets | 2B | A+ | 2003-2008 | C | University of Texas-San Antonio | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 35 | 1054 | June-Reg | James Newman | New York Mets | 2B | RK | 2006-2007 | C | Erskine College | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 36 | 1084 | June-Reg | Edgar Ramirez | New York Mets | P | AAA | 2003-2012 | C | Louisiana State University | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 37 | 1114 | June-Reg | Joshua Stinson | New York Mets | P | MLB | 2006-2013 | H | Northwood (Shreveport,LA) | SF | LA | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 0 | 2 | 4.43 | 1 | 22 | 11 | 1 |
| 2006 | 38 | 1144 | June-Reg | J.J. Leaper | New York Mets | P | A+ | 2006-2011 | H | Sentinel (Sentinel,OK) | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 39 | 1174 | June-Reg | Donald Green | New York Mets | OF | RK | 2005-2007 | C | Texas Southern University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 40 | 1204 | June-Reg | Tyler Binkley | New York Mets | P | - | H | St. Mary's (null) | SF | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | ||
| 2006 | 41 | 1234 | June-Reg | Victor Black ** | New York Mets | P | AAA | 2008-2013 | H | Amarillo (Amarillo,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 42 | 1264 | June-Reg | Terrell Stringer | New York Mets | P | NCAA | 2009-2010 | H | Smiths Station (Smiths,AL) | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 43 | 1293 | June-Reg | Albert Cartwright ** | New York Mets | 2B | AA | 2007-2013 | H | American Heritage (Plantation,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 44 | 1322 | June-Reg | Brad Schwarzenbach | New York Mets | P | NCAA | 2007-2007 | C | Cerritos College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 45 | 1351 | June-Reg | Beau Pender | New York Mets | P | NCAA | 2008-2010 | C | Florida Gulf Coast University | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 46 | 1379 | June-Reg | Kyle Johnson | New York Mets | P | RK | 2006-2007 | C | Chapman University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 47 | 1407 | June-Reg | Shay Conder | New York Mets | C | NCAA | 2006-2006 | C | College of Southern Nevada | SF | NV | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 48 | 1435 | June-Reg | Jon Koller | New York Mets | P | RK | 2002-2006 | C | Oregon State University | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 49 | 1463 | June-Reg | Johnny Monell ** | New York Mets | C | AAA | 2007-2013 | C | Seminole State College of Florida | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 2006 | 50 | 1491 | June-Reg | Ryan Wolfe | New York Mets | P | Ind | 2009-2010 | H | Winter Park (Winter Park,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |