| 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 | 1 | 1 | June-Reg | Josh Hamilton | Tampa Bay Rays | OF | MLB | 1999-2013 | H | Athens Drive (Raleigh,NC) | SF | NC | 2825 | 173 | 19 | 161 | 553 | 43 | .304 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 2 | June-Reg | Josh Beckett | Florida Marlins | P | MLB | 2000-2013 | H | Spring (Spring,TX) | SF | TX | 242 | 9 | 0 | 3 | 16 | 0 | .136 | 132 | 95 | 3.91 | 0 | 1892 | 1753 | 304 |
| 1999 | 1 | 3 | June-Reg | Eric Munson | Detroit Tigers | C-1B | MLB | 1997-2011 | C | USC | SF | CA | 1056 | 37 | 3 | 49 | 147 | 4 | .214 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 4 | June-Reg | Corey Myers | Arizona Diamondbacks | IF | AAA | 1999-2007 | H | Desert Vista (Phoenix,AZ) | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 5 | June-Reg | B.J. Garbe | Minnesota Twins | OF | AA | 1999-2006 | H | Moses Lake (Moses Lake,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 6 | June-Reg | Josh Girdley | Montreal Expos | P | A+ | 1999-2004 | H | Jasper (Jasper,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 7 | June-Reg | Kyle Snyder | Kansas City Royals | P | MLB | 1997-2011 | C | University of North Carolina | SF | NC | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 8 | 17 | 5.57 | 0 | 238 | 157 | 29 |
| 1999 | 1 | 8 | June-Reg | Bobby Bradley | Pittsburgh Pirates | P | AAA | 1999-2005 | H | Wellington Christian (Wellington,FL) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 9 | June-Reg | Barry Zito | Oakland Athletics | P | MLB | 1997-2013 | C | USC | SF | CA | 310 | 0 | 0 | 0 | 9 | 0 | .097 | 160 | 132 | 3.93 | 0 | 2436 | 1797 | 394 |
| 1999 | 1 | 10 | June-Reg | Ben Sheets | Milwaukee Brewers | P | MLB | 1999-2012 | C | University of Louisiana-Monroe | SF | LA | 449 | 3 | 0 | 0 | 12 | 0 | .076 | 94 | 96 | 3.78 | 0 | 1597 | 1325 | 250 |
| 1999 | 1 | 11 | June-Reg | Ryan Christianson | Seattle Mariners | C | AAA | 1999-2007 | H | Arlington (Riverside,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 12 | June-Reg | Brett Myers | Philadelphia Phillies | P | MLB | 1999-2013 | C | Jacksonville University | SF | FL | 471 | 11 | 0 | 0 | 12 | 0 | .134 | 97 | 93 | 4.20 | 40 | 1689 | 1367 | 249 |
| 1999 | 1 | 13 | June-Reg | Mike Paradis | Baltimore Orioles | P | AAA | 1997-2004 | C | Clemson University | SF | SC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 14 | June-Reg | Ty Howington | Cincinnati Reds | P | AA | 2000-2005 | H | Hudson's Bay (Vancouver,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 15 | June-Reg | Jason Stumm | Chicago White Sox | P | AA | 1999-2005 | H | Centralia (Centralia,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 16 | June-Reg | Jason Jennings | Colorado Rockies | P | MLB | 1997-2011 | C | Baylor University | SF | TX | 329 | 14 | 0 | 2 | 26 | 0 | .207 | 62 | 74 | 4.95 | 1 | 1128 | 749 | 180 |
| 1999 | 1 | 17 | June-Reg | Rick Asadoorian | Boston Red Sox | OF | AAA | 2000-2011 | H | Northrbridge (Northrbridge,MA) | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 18 | June-Reg | Rich Stahl | Baltimore Orioles | P | AAA | 2000-2006 | H | Newton (Covington,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 19 | June-Reg | Alex Rios | Toronto Blue Jays | OF | MLB | 1999-2013 | H | -- | SF | 4926 | 289 | 49 | 143 | 627 | 185 | .278 | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 1 | 20 | June-Reg | Vince Faison | San Diego Padres | OF | AAA | 1999-2007 | H | Toombs County (Lyons,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 21 | June-Reg | Larry Bigbie | Baltimore Orioles | OF | MLB | 1997-2010 | C | Ball State University | SF | IN | 1227 | 56 | 4 | 31 | 137 | 25 | .267 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 22 | June-Reg | Matt Ginter | Chicago White Sox | P | MLB | 1997-2009 | C | Mississippi State University | SF | MS | 14 | 1 | 0 | 0 | 1 | 0 | .214 | 5 | 7 | 5.43 | 1 | 232 | 132 | 19 |
| 1999 | 1 | 23 | June-Reg | Keith Reed | Baltimore Orioles | OF | MLB | 1999-2008 | C | Providence College | SF | RI | 5 | 0 | 0 | 0 | 1 | 0 | .200 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 24 | June-Reg | Kurt Ainsworth | San Francisco Giants | P | MLB | 1997-2004 | C | Louisiana State University | SF | LA | 28 | 1 | 0 | 0 | 0 | 0 | .071 | 6 | 8 | 5.19 | 0 | 127 | 90 | 22 |
| 1999 | 1 | 25 | June-Reg | Mike MacDougal | Kansas City Royals | P | MLB | 1997-2013 | C | Wake Forest University | SF | NC | -- | -- | -- | -- | -- | -- | -- | 18 | 23 | 4.00 | 71 | 394 | 325 | 3 |
| 1999 | 1 | 26 | June-Reg | Ben Christensen | Chicago Cubs | P | AA | 1999-2004 | C | Wichita State University | SF | KS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 27 | June-Reg | David Walling | New York Yankees | P | AAA | 1997-2002 | C | University of Arkansas | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 28 | June-Reg | Gerik Baxter | San Diego Padres | P | A | 1999-2000 | H | Edmonds-Woodway (Edmonds,WA) | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 29 | June-Reg | Omar Ortiz | San Diego Padres | P | AA | 1997-2003 | C | University of Texas-Pan American | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 30 | June-Reg | Chance Caple | St. Louis Cardinals | P | A+ | 1998-2004 | C | Texas A&M University | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 31 | June-Reg | Casey Daigle | Arizona Diamondbacks | P | MLB | 2000-2011 | H | Sulphur (Sulphur,LA) | SF | LA | 18 | 2 | 0 | 0 | 0 | 0 | .111 | 3 | 4 | 7.16 | 0 | 72 | 30 | 10 |
| 1999 | 1 | 32 | June-Reg | Jay Gehrke | Kansas City Royals | P | A+ | 1999-2001 | C | Pepperdine University | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 33 | June-Reg | Jeff Heaverlo | Seattle Mariners | P | AAA | 1999-2007 | C | University of Washington | SF | WA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 34 | June-Reg | Joshua Cenate | Baltimore Orioles | P | A- | 1999-2003 | H | Jefferson (Shenandoah Junction,WV) | SF | WV | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 35 | June-Reg | Brian West | Chicago White Sox | P | AAA | 1999-2006 | H | West Monroe (West Monroe,LA) | SF | LA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 36 | June-Reg | Nick Stocks | St. Louis Cardinals | P | AAA | 1998-2006 | C | Florida State University | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 37 | June-Reg | Jason Repko | Los Angeles Dodgers | OF | MLB | 1999-2012 | H | Hanford (Richland,WA) | SF | WA | 700 | 29 | 4 | 16 | 67 | 27 | .224 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 38 | June-Reg | Colby Lewis | Texas Rangers | P | MLB | 1999-2012 | C | Bakersfield College | SF | CA | 20 | 1 | 0 | 0 | 4 | 0 | .250 | 44 | 44 | 4.76 | 0 | 724 | 613 | 114 |
| 1999 | 1 | 39 | June-Reg | Jerome Williams | San Francisco Giants | P | MLB | 1999-2013 | H | Waipahu (Waipahu, HI) | SF | HI | 120 | 3 | 0 | 0 | 1 | 0 | .117 | 33 | 37 | 4.29 | 1 | 607 | 384 | 92 |
| 1999 | 1 | 40 | June-Reg | Brad Baker | Boston Red Sox | P | AAA | 1999-2007 | H | Pioneer Valley Regional (Northfield,MA) | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 41 | June-Reg | Casey Burns | San Diego Padres | P | A | 1999-2001 | C | University of Richmond | SF | VA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 42 | June-Reg | Mike Rosamond | Houston Astros | OF | AAA | 1997-2006 | C | University of Mississippi | SF | MS | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 43 | June-Reg | Jimmy Gobble | Kansas City Royals | P | MLB | 1999-2010 | H | Battle (Bristol,VA) | SF | VA | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 22 | 23 | 5.29 | 4 | 436 | 285 | 43 |
| 1999 | 1 | 44 | June-Reg | Scott Rice | Baltimore Orioles | P | MLB | 1999-2013 | H | Royal (Simi Valley,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 45 | June-Reg | Rob Purvis | Chicago White Sox | P | AAA | 1997-2005 | C | Bradley University | SF | IL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 46 | June-Reg | Chris Duncan | St. Louis Cardinals | IF | MLB | 1999-2010 | H | Canyon del Oro (Tucson,AZ) | SF | AZ | 1147 | 55 | 5 | 55 | 175 | 4 | .257 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 47 | June-Reg | David Mead | Texas Rangers | P | A+ | 2000-2004 | H | Soddy-Daisy (Soddy-Daisy,TN) | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 48 | June-Reg | Casey Fossum | Boston Red Sox | P | MLB | 1998-2011 | C | Texas A&M University | SF | TX | 46 | 0 | 0 | 0 | 0 | 0 | .087 | 40 | 53 | 5.45 | 2 | 786 | 607 | 120 |
| 1999 | 1 | 49 | June-Reg | Mike Bynum | San Diego Padres | P | MLB | 1997-2005 | C | University of North Carolina | SF | NC | 18 | 0 | 0 | 0 | 0 | 0 | .167 | 2 | 5 | 7.73 | 0 | 64 | 52 | 8 |
| 1999 | 1 | 50 | June-Reg | Brian Roberts | Baltimore Orioles | SS | MLB | 1997-2013 | C | University of South Carolina | SF | SC | 4949 | 339 | 34 | 84 | 482 | 275 | .280 | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 1 | 51 | June-Reg | Nick Trzesniak | San Diego Padres | C | AAA | 1999-2008 | H | Andrew (Tinley Park,IL) | SF | IL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |