| 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 |
| 1998 | 1 | 1 | June-Reg | Pat Burrell | Philadelphia Phillies | 1B | MLB | 1996-2011 | C | University of Miami | SF | FL | 5503 | 299 | 16 | 292 | 976 | 7 | .253 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 2 | June-Reg | Mark Mulder | Oakland Athletics | P | MLB | 1999-2008 | C | Michigan State University | SF | MI | 111 | 2 | 0 | 1 | 9 | 0 | .162 | 103 | 60 | 4.18 | 0 | 1314 | 834 | 203 |
| 1998 | 1 | 3 | June-Reg | Corey Patterson | Chicago Cubs | OF | MLB | 1999-2012 | H | Harrison (Kennesaw,GA) | SF | GA | 4171 | 197 | 34 | 118 | 431 | 218 | .252 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 4 | June-Reg | Jeff Austin | Kansas City Royals | P | MLB | 1996-2005 | C | Stanford University | SF | CA | 8 | 0 | 0 | 0 | 0 | 0 | .125 | 2 | 3 | 6.75 | 0 | 65 | 55 | 7 |
| 1998 | 1 | 5 | June-Reg | J.D. Drew | St. Louis Cardinals | OF | MLB | 1995-2011 | H | Lowndes (Valdosta,GA) | SF | 5173 | 273 | 48 | 242 | 795 | 87 | .278 | -- | -- | -- | -- | -- | -- | -- | |
| 1998 | 1 | 6 | June-Reg | Ryan Mills | Minnesota Twins | P | AAA | 1996-2004 | C | Arizona State University | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 7 | June-Reg | Austin Kearns | Cincinnati Reds | OF | MLB | 1998-2013 | H | Lafayette (Lexington,KY) | SF | KY | 3579 | 187 | 13 | 121 | 494 | 33 | .254 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 8 | June-Reg | Felipe Lopez | Toronto Blue Jays | 3B | MLB | 1998-2011 | H | Lake Brantley (Altamonte Springs,FL) | SF | FL | 4337 | 219 | 31 | 90 | 439 | 124 | .264 | 0 | 0 | 0.00 | 0 | 1 | 0 | 0 |
| 1998 | 1 | 9 | June-Reg | Sean Burroughs | San Diego Padres | 3B | MLB | 1999-2012 | H | Wilson (Long Beach,CA) | SF | CA | 1664 | 68 | 12 | 12 | 143 | 20 | .278 | 0 | 0 | 27.00 | 0 | 1 | 0 | 0 |
| 1998 | 1 | 10 | June-Reg | Carlos Pena | Texas Rangers | 1B | MLB | 1998-2013 | C | Northeastern University | SF | MA | 4610 | 215 | 25 | 277 | 791 | 27 | .234 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 11 | June-Reg | Josh McKinley | Montreal Expos | IF | AA | 1998-2004 | H | Malvern Preparatory Schoo (Malvern,PA) | SF | PA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 12 | June-Reg | Adam Everett | Boston Red Sox | SS | MLB | 1996-2011 | C | University of South Carolina | SF | SC | 2758 | 135 | 15 | 40 | 283 | 67 | .242 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 13 | June-Reg | J.M. Gold | Milwaukee Brewers | P | A+ | 1998-2003 | H | Toms River North (Toms River,NJ) | SF | NJ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 14 | June-Reg | Jeff Weaver | Detroit Tigers | P | MLB | 1996-2010 | C | Fresno State University | SF | CA | 208 | 6 | 1 | 0 | 13 | 0 | .207 | 104 | 119 | 4.71 | 2 | 1838 | 1214 | 274 |
| 1998 | 1 | 15 | June-Reg | Clint Johnston | Pittsburgh Pirates | 1B | AA | 1996-2008 | C | Vanderbilt University | SF | TN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 16 | June-Reg | Kip Wells | Chicago White Sox | P | MLB | 1996-2013 | C | Baylor University | SF | TX | 331 | 10 | 1 | 4 | 17 | 1 | .190 | 69 | 103 | 4.71 | 2 | 1338 | 963 | 219 |
| 1998 | 1 | 17 | June-Reg | Brad Lidge | Houston Astros | P | MLB | 1996-2012 | C | University of Notre Dame | SF | IN | 7 | 1 | 0 | 0 | 2 | 0 | .286 | 26 | 32 | 3.54 | 225 | 603 | 799 | 1 |
| 1998 | 1 | 18 | June-Reg | Seth Etherton | Anaheim Angels | P | MLB | 1995-2011 | C | USC | SF | CA | 9 | 0 | 0 | 0 | 0 | 0 | .111 | 9 | 7 | 6.30 | 0 | 116 | 63 | 23 |
| 1998 | 1 | 19 | June-Reg | Tony Torcato | San Francisco Giants | OF | MLB | 1998-2008 | H | Woodland (Woodland,CA) | SF | CA | 47 | 2 | 0 | 0 | 3 | 0 | .298 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 20 | June-Reg | C.C. Sabathia | Cleveland Indians | P | MLB | 1998-2013 | H | Vallejo (Vallejo,CA) | SF | CA | 105 | 3 | 0 | 3 | 14 | 0 | .238 | 191 | 102 | 3.50 | 0 | 2564 | 2214 | 383 |
| 1998 | 1 | 21 | June-Reg | Jason Tyner | New York Mets | OF | MLB | 1998-2009 | C | Texas A&M University | SF | TX | 1358 | 41 | 11 | 1 | 94 | 61 | .275 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 22 | June-Reg | Matt Thornton | Seattle Mariners | P | MLB | 1998-2013 | C | Grand Valley State University | SF | MI | 1 | 0 | 0 | 0 | 0 | 0 | .000 | 32 | 38 | 3.51 | 23 | 525 | 552 | 1 |
| 1998 | 1 | 23 | June-Reg | Bubba Crosby | Los Angeles Dodgers | OF | MLB | 1998-2007 | C | Rice University | SF | TX | 250 | 5 | 2 | 4 | 20 | 10 | .216 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 24 | June-Reg | Andy Brown | New York Yankees | OF | AA | 1998-2005 | H | Richmond (Richmond,IN) | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 25 | June-Reg | Nate Bump | San Francisco Giants | P | MLB | 1995-2011 | C | Penn State University | SF | PA | 10 | 0 | 0 | 0 | 0 | 0 | .100 | 6 | 7 | 4.68 | 1 | 148 | 79 | 2 |
| 1998 | 1 | 26 | June-Reg | Rick Elder | Baltimore Orioles | OF | A+ | 1998-2006 | H | Sprayberry (Marietta,GA) | SF | GA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 27 | June-Reg | Chip Ambres ** | Florida Marlins | OF | MLB | 1999-2009 | H | West Brook (Beaumont,TX) | SF | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1998 | 1 | 28 | June-Reg | Matt Roney | Colorado Rockies | P | MLB | 1998-2007 | H | Edmond North (Edmond,OK) | SF | OK | 2 | 0 | 0 | 0 | 0 | 0 | .500 | 1 | 10 | 5.42 | 0 | 105 | 47 | 11 |
| 1998 | 1 | 29 | June-Reg | Arturo McDowell | San Francisco Giants | OF | AA | 1998-2002 | H | Forest Hill (Jackson,MS) | SF | FL | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 30 | June-Reg | Matt Burch | Kansas City Royals | P | AA | 1998-2004 | C | Virginia Commonwealth University | SF | VA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 31 | June-Reg | Chris George | Kansas City Royals | P | MLB | 1998-2012 | H | Klein (Klein,TX) | SF | TX | 3 | 0 | 0 | 0 | 1 | 0 | .333 | 14 | 20 | 6.48 | 0 | 237 | 99 | 44 |
| 1998 | 1 | 32 | June-Reg | Ben Diggins ** | St. Louis Cardinals | P | MLB | 1999-2006 | H | Bradshaw Mountain (Prescott Valley,AZ) | SF | AZ | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 33 | June-Reg | Brad Wilkerson | Montreal Expos | OF | MLB | 1996-2009 | C | University of Florida | SF | FL | 3187 | 193 | 28 | 122 | 399 | 53 | .247 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 34 | June-Reg | Nate Cornejo | Detroit Tigers | P | MLB | 1998-2006 | H | Wellington (Wellington,KS) | SF | KS | 4 | 0 | 0 | 0 | 0 | 0 | .000 | 12 | 29 | 5.41 | 0 | 313 | 103 | 56 |
| 1998 | 1 | 35 | June-Reg | Aaron Rowand | Chicago White Sox | OF | MLB | 1996-2011 | C | Cal State Fullerton | SF | CA | 4374 | 267 | 18 | 136 | 536 | 67 | .273 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 36 | June-Reg | Choo Freeman | Colorado Rockies | OF | MLB | 1998-2007 | C | University of Dallas | SF | TX | 285 | 10 | 6 | 3 | 29 | 6 | .225 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 37 | June-Reg | Mike Nannini | Houston Astros | P | AAA | 1998-2008 | H | Green Valley (Henderson,NV) | SF | NV | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 38 | June-Reg | Chris Jones | San Francisco Giants | P | AA | 1998-2003 | H | South Mecklenburg (Charlotte,NC) | SF | NC | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 39 | June-Reg | Mamon Tucker | Baltimore Orioles | OF | AA | 1998-2005 | H | Austin (Austin,TX) | SF | TX | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 40 | June-Reg | Jeff Winchester | Colorado Rockies | C | AA | 1998-2006 | H | Archbishop Rummel (Metairie,LA) | SF | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | |
| 1998 | 1 | 41 | June-Reg | Jeff Urban | San Francisco Giants | P | AAA | 1998-2007 | C | Ball State University | SF | IN | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 42 | June-Reg | Eric Valent | Philadelphia Phillies | OF | MLB | 1998-2006 | C | UCLA | SF | CA | 406 | 20 | 2 | 13 | 37 | 0 | .234 | -- | -- | -- | -- | -- | -- | -- |
| 1998 | 1 | 43 | June-Reg | Mark Prior ** | New York Yankees | P | MLB | 1999-2013 | H | University of San Diego (San Diego,CA) | SF | CA | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |