| 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 | 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 | 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 | 2 | 62 | June-Reg | John Thomas | San Francisco Giants | P | AAA | 2001-2006 | H | Righetti (Santa Maria,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 2 | 75 | June-Reg | Jack Taschner | San Francisco Giants | P | MLB | 1999-2010 | C | University of Wisconsin | SF | WI | 2 | 0 | 0 | 0 | 0 | 0 | .000 | 10 | 5 | 5.14 | 0 | 189 | 160 | 0 |
| 1999 | 3 | 108 | June-Reg | Sean McGowan | San Francisco Giants | IF | AAA | 1999-2004 | C | Boston College | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 4 | 138 | June-Reg | Jeremy Cunningham | San Francisco Giants | P | A+ | 1999-2001 | C | Cal Poly | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 5 | 168 | June-Reg | Ryan Cox | San Francisco Giants | P | AAA | 1999-2003 | C | Southern Illinois University | SF | IL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 6 | 198 | June-Reg | Ryan Pini ** | San Francisco Giants | OF | A+ | 1999-2002 | C | Dixie State College of Utah | SF | UT | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 7 | 228 | June-Reg | Joe Jester | San Francisco Giants | IF | AAA | 1998-2003 | C | University of Arkansas | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 8 | 258 | June-Reg | Kevin Vent | San Francisco Giants | P | AAA | 1999-2003 | C | University of Arkansas | SF | AR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 9 | 288 | June-Reg | Josh Cook | San Francisco Giants | SS | A+ | 1999-2001 | C | Yuba Community College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 10 | 318 | June-Reg | Anthony Yacco | San Francisco Giants | P | A+ | 1999-2003 | H | Mahopac (Mahopac,NY) | SF | NY | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 11 | 348 | June-Reg | Jeff Verplancke | San Francisco Giants | P | AAA | 2000-2002 | C | Cal State Los Angeles | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 12 | 378 | June-Reg | Ronnie Merrill ** | San Francisco Giants | IF | AAA | 1997-2008 | C | University of Tampa | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 13 | 408 | June-Reg | Fletcher Lee | San Francisco Giants | P | A+ | 1999-2000 | C | Lewis and Clark College | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 14 | 438 | June-Reg | Mike Meyer ** | San Francisco Giants | P | A+ | 1997-2006 | C | University of Arizona | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 15 | 468 | June-Reg | Harold Featherstone | San Francisco Giants | P | A+ | 1999-2001 | C | North Carolina A&T State University | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 16 | 498 | June-Reg | Micah Holst | San Francisco Giants | OF | AAA | 1996-2004 | C | Missouri State University | SF | MO | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 17 | 528 | June-Reg | Vance Cozier | San Francisco Giants | P | AA | 1999-2003 | C | St. Bonaventure University | SF | NY | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 18 | 558 | June-Reg | Brian Meagher | San Francisco Giants | P | A- | 1999-1999 | C | College of San Mateo | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 19 | 588 | June-Reg | Ryan Cheo | San Francisco Giants | P | NCAA | 2002-2002 | C | Saddleback College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 20 | 618 | June-Reg | Anthony Turco | San Francisco Giants | C | AA | 2000-2003 | C | St. Petersburg College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 21 | 648 | June-Reg | Ryan Luther | San Francisco Giants | C | AAA | 1999-2008 | C | Lewis and Clark College | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 22 | 678 | June-Reg | Jason Barrow | San Francisco Giants | OF | - | C | Chemeketa Community College | SF | OR | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 23 | 708 | June-Reg | Michael Zirelli | San Francisco Giants | P | A+ | 1996-2004 | C | Cal Poly | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 24 | 738 | June-Reg | Bill Murphy ** | San Francisco Giants | P | MLB | 2002-2012 | H | Arlington (Riverside,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 25 | 768 | June-Reg | Andrew Edwards ** | San Francisco Giants | P | A- | 2002-2007 | H | Christ the King (Flushing,NY) | SF | NY | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 26 | 798 | June-Reg | Kevin Alexander | San Francisco Giants | IF | A+ | 2000-2003 | C | Modesto Junior College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 27 | 828 | June-Reg | Troy Gustafson | San Francisco Giants | LF | A+ | 2000-2001 | H | Blaine (Blaine,MN) | SF | MN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 28 | 858 | June-Reg | Lars Hansen | San Francisco Giants | C | NCAA | 1998-1999 | C | University of Hawaii | SF | HI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 29 | 888 | June-Reg | Troy Ransom | San Francisco Giants | P | A+ | 1999-2003 | C | South Mountain Community College | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 30 | 918 | June-Reg | Ryan Davis | San Francisco Giants | A+ | 1998-2001 | C | Cosumnes River College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 31 | 948 | June-Reg | Scott Daeley | San Francisco Giants | AA | 1998-2001 | C | Wake Forest University | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 32 | 978 | June-Reg | Tim Gilhooly ** | San Francisco Giants | OF | A- | 2002-2003 | H | San Ramon Valley (Danville,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 33 | 1008 | June-Reg | Kavonski Chatman | San Francisco Giants | P-CF | - | C | Northeast Texas Community College | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 34 | 1038 | June-Reg | Scott Shoemaker ** | San Francisco Giants | AAA | 2003-2008 | H | Granite Hills (El Cajon,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 35 | 1068 | June-Reg | Robert Lorona | San Francisco Giants | SS | - | H | Hayden (Winkelman,AZ) | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 36 | 1098 | June-Reg | Bryan Lang | San Francisco Giants | OF | - | C | Scottsdale Community College | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 37 | 1128 | June-Reg | Chris Norris | San Francisco Giants | P | NCAA | 1999-2000 | C | Central Arizona College | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 38 | 1158 | June-Reg | Drew Endicott ** | San Francisco Giants | P | AA | 2000-2006 | H | Carthage (Carthage,MO) | SF | MO | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 39 | 1188 | June-Reg | Paul Turco | San Francisco Giants | A+ | 1996-2000 | C | Auburn University | SF | AL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 40 | 1218 | June-Reg | Travis Veracka ** | San Francisco Giants | NCAA | 1999-2000 | C | University of Massachusetts | SF | MA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 41 | 1247 | June-Reg | Winston Woods | San Francisco Giants | CF | - | C | Broward College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 42 | 1275 | June-Reg | Jason Hickman ** | San Francisco Giants | RK | 2000-2002 | C | Ball State University | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 43 | 1302 | June-Reg | Brett Cayton | San Francisco Giants | P | NCAA | 2002-2003 | H | Fountain Valley (Fountain Valley,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 44 | 1329 | June-Reg | Daniel August | San Francisco Giants | P | NCAA | 2000-2000 | C | St. Petersburg College | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 45 | 1354 | June-Reg | Chad Ashlock ** | San Francisco Giants | P | A- | 2000-2001 | C | University of Texas | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 46 | 1378 | June-Reg | Wes Faust | San Francisco Giants | P | A | 2000-2006 | C | Oklahoma Baptist University | SF | OK | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 47 | 1402 | June-Reg | Oscar Vargas | San Francisco Giants | Ind | 2003-2005 | C | Chabot College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 48 | 1426 | June-Reg | Jamie Aloy | San Francisco Giants | 1B | NCAA | 1997-2000 | C | University of Hawaii | SF | HI | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1999 | 49 | 1449 | June-Reg | Josh Sousa | San Francisco Giants | P | - | C | Modesto Junior College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1999 | 50 | 1470 | June-Reg | Brian Grochol | San Francisco Giants | OF | A- | 1999-1999 | C | Canada College | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |