| 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 |
| 1999 | 3 | 85 | June-Reg | Doug Waechter | Tampa Bay Rays | P | MLB | 1999-2009 | H | Northeast (St. Petersburg,FL) | SF | FL | 8 | 0 | 0 | 0 | 0 | 0 | .125 | 18 | 27 | 5.34 | 0 | 384 | 226 | 54 |
| 1999 | 3 | 86 | June-Reg | Josh Wilson | Florida Marlins | SS | MLB | 1999-2013 | H | Mount Lebanon (Pittsburgh,PA) | SF | PA | 930 | 46 | 6 | 9 | 67 | 13 | .227 | 0 | 1 | 9.00 | 0 | 3 | 0 | 0 |
| 1999 | 3 | 87 | June-Reg | Neil Jenkins | Detroit Tigers | 1B-3B | AA | 1999-2004 | H | Dwyer (West Palm Beach,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 88 | June-Reg | Rich Rundles | Boston Red Sox | P | MLB | 1999-2012 | H | Jefferson County (New Market,TN) | SF | TN | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 1.50 | 0 | 6 | 7 | 0 |
| 1999 | 3 | 89 | June-Reg | Justin Morneau | Minnesota Twins | 1B | MLB | 1999-2013 | H | New Westminster (New Westminster,BC) | SF | BC | 4254 | 257 | 16 | 204 | 786 | 5 | .280 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 90 | June-Reg | Drew McMillan | Montreal Expos | C | AA | 1999-2005 | H | El Dorado (Placentia,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 91 | June-Reg | Kiki Bengochea ** | Kansas City Royals | P | A+ | 2000-2004 | H | Columbus (Miami,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 92 | June-Reg | Aron Weston | Pittsburgh Pirates | RF-CF | AA | 1999-2006 | H | Solon (Solon,OH) | SF | IA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 93 | June-Reg | Jorge Soto | Oakland Athletics | C | A+ | 1999-2003 | C | Troy University | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 94 | June-Reg | Ruddy Lugo | Milwaukee Brewers | P | MLB | 1999-2011 | H | Xaverian (Brooklyn,NY) | SF | NY | -- | -- | -- | -- | -- | -- | -- | 8 | 4 | 4.39 | 0 | 133 | 82 | 0 |
| 1999 | 3 | 95 | June-Reg | Willie Bloomquist | Seattle Mariners | IF | MLB | 1997-2012 | C | Arizona State University | SF | AZ | 2550 | 98 | 22 | 17 | 193 | 131 | .269 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 96 | June-Reg | Russ Jacobson | Philadelphia Phillies | C | AAA | 1998-2005 | C | University of Miami | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 97 | June-Reg | Sheldon Fulse | Seattle Mariners | OF | AA | 1999-2008 | H | Jenkins (Lakeland,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 98 | June-Reg | Brandon Love | Cincinnati Reds | P | A | 1999-2000 | H | Viola (Viola,AR) | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 99 | June-Reg | Jon Rauch | Chicago White Sox | P | MLB | 1999-2013 | C | Morehead State University | SF | KY | 21 | 0 | 0 | 1 | 3 | 0 | .095 | 42 | 38 | 3.80 | 62 | 578 | 460 | 11 |
| 1999 | 3 | 100 | June-Reg | Josh Bard | Colorado Rockies | C | MLB | 1997-2012 | C | Texas Tech University | SF | TX | 1778 | 109 | 3 | 39 | 220 | 1 | .254 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 101 | June-Reg | Phil Wilson | Anaheim Angels | P | AA | 2000-2007 | H | Poway (Poway,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 102 | June-Reg | B.R. Cook | St. Louis Cardinals | P | AAA | 1998-2004 | C | Oregon State University | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 103 | June-Reg | Matt Ford | Toronto Blue Jays | P | MLB | 1999-2008 | H | Taravella (Coral Springs,FL) | SF | FL | 7 | 1 | 0 | 0 | 1 | 0 | .143 | 0 | 3 | 4.33 | 0 | 44 | 26 | 4 |
| 1999 | 3 | 104 | June-Reg | Jon Kessick | Baltimore Orioles | C | A+ | 1999-2002 | C | Ball State University | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 105 | June-Reg | Hank Blalock | Texas Rangers | 3B | MLB | 1999-2010 | H | Rancho Bernardo (San Diego,CA) | SF | CA | 3567 | 198 | 17 | 153 | 542 | 14 | .269 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 106 | June-Reg | Jeremy Griffiths | New York Mets | P | MLB | 1997-2005 | C | University of Toledo | SF | OH | 10 | 0 | 0 | 0 | 0 | 0 | .000 | 1 | 4 | 7.35 | 0 | 45 | 30 | 7 |
| 1999 | 3 | 107 | June-Reg | Eric Johnson | Cleveland Indians | RF | AA | 1999-2004 | C | Western Carolina University | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 108 | June-Reg | Sean McGowan | San Francisco Giants | IF | AAA | 1999-2004 | C | Boston College | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 109 | June-Reg | Antron Seiber | Boston Red Sox | OF | A+ | 1999-2003 | H | Independence (Independence,LA) | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 110 | June-Reg | Ryan Gripp | Chicago Cubs | 3B | AA | 1999-2007 | C | Creighton University | SF | NE | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 111 | June-Reg | Alex Graman | New York Yankees | P | MLB | 1999-2011 | C | Indiana State University | SF | IN | -- | -- | -- | -- | -- | -- | -- | 0 | 0 | 18.47 | 0 | 6 | 4 | 2 |
| 1999 | 3 | 112 | June-Reg | Joshua Vitek | San Diego Padres | P | A- | 1999-2001 | H | Fayetteville (Fayetteville,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 113 | June-Reg | Jimmy Barrett | Houston Astros | P | A+ | 1999-2003 | H | Fort Hill (Cumberland,MD) | SF | MD | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 3 | 114 | June-Reg | Pat Manning | Atlanta Braves | IF | A+ | 1999-2002 | H | Mater Dei (Santa Ana,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |