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| First Round Draft Pick History |
| 1 | 1 | 1 | 1995 | Inaugural Draft | OF | Barry | Bonds | MLB |
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| Complete Draft History |
| 2 | 16 | 40 | 2001 | Annual Draft | OF | Jay | Gibbons | MLB |
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| 4 | 16 | 88 | 2001 | Annual Draft | P | Josh | Fogg | MLB |
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| 5 | 16 | 112 | 2001 | Annual Draft | P | Ryan | Jensen | MLB |
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| 6 | 16 | 136 | 2001 | Annual Draft | P | Dennis | Stark | MLB |
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| 6 | 24 | 144 | 2001 | Annual Draft | C | Tom | Wilson | MLB |
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| 7 | 16 | 160 | 2001 | Annual Draft | P | Kurt | Ainsworth | MLB |
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| 8 | 16 | 184 | 2001 | Annual Draft | P | Blaine | Neal | MLB |
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| 9 | 16 | 208 | 2001 | Annual Draft | 1B | Kevin | Witt | MLB |
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| 10 | 16 | 232 | 2001 | Annual Draft | P | Eric | Knott | MLB |
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| 11 | 16 | 256 | 2001 | Annual Draft | P | Robert | Ellis | MLB |
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| 12 | 16 | 280 | 2001 | Annual Draft | P | Mike | Bacsik | MLB |
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| 13 | 16 | 304 | 2001 | Annual Draft | P | Craig | Dingman | MLB |
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| 14 | 16 | 328 | 2001 | Annual Draft | P | Jason | Standridge | MLB |
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| 15 | 16 | 352 | 2001 | Annual Draft | P | Brad | Thomas | MLB |
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| 16 | 16 | 376 | 2001 | Annual Draft | | SKIPPED | PICK | MLB |
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| 2 | 17 | 41 | 2000 | Annual Draft | P | Jose | Mercedes | MLB |
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| 4 | 17 | 89 | 2000 | Annual Draft | OF | Timo | Perez | MLB |
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| 5 | 17 | 113 | 2000 | Annual Draft | 1B+ | Morgan | Burkhart | MLB |
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| 6 | 17 | 137 | 2000 | Annual Draft | 1B+ | Julio | Zuleta | MLB |
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| 7 | 17 | 161 | 2000 | Annual Draft | P | Travis | Harper | MLB |
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| 8 | 17 | 185 | 2000 | Annual Draft | OF+ | Israel | Alcantara | MLB |
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| 4 | 23 | 95 | 1999 | Annual Draft | P | Kevin | Jarvis | MLB |
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| 6 | 23 | 143 | 1999 | Annual Draft | P | John | Bale | MLB |
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| 7 | 23 | 167 | 1999 | Annual Draft | 2B | Jay | Canizaro | MLB |
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| 8 | 23 | 191 | 1999 | Annual Draft | P | Doug | Creek | MLB |
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| 9 | 23 | 215 | 1999 | Annual Draft | P | Joe | Slusarski | MLB |
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| 10 | 23 | 239 | 1999 | Annual Draft | P | Michael | Tejera | MLB |
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| 11 | 23 | 263 | 1999 | Annual Draft | | SKIPPED | PICK | MLB |
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| 3 | 18 | 66 | 1998 | Annual Draft | 3B+ | Dave | Berg | MLB |
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| 3 | 20 | 68 | 1998 | Annual Draft | OF | Armando | Rios | MLB |
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| 4 | 20 | 92 | 1998 | Annual Draft | C | A.J. | Hinch | MLB |
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| 5 | 13 | 109 | 1998 | Annual Draft | OF+ | Matt | Luke | MLB |
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| 5 | 20 | 116 | 1998 | Annual Draft | C+ | Mark | Dalesandro | MLB |
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| 6 | 20 | 140 | 1998 | Annual Draft | P | Stan | Spencer | MLB |
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| 7 | 20 | 164 | 1998 | Annual Draft | 1B+ | Jack | Howell | MLB |
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| 8 | 20 | 188 | 1998 | Annual Draft | OF | Brian | Simmons | MLB |
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| 9 | 20 | 212 | 1998 | Annual Draft | SS+ | Luis | Rivera | MLB |
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| 2 | 22 | 46 | 1997 | Annual Draft | OF | Rob | Ducey | MLB |
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| 3 | 19 | 67 | 1997 | Annual Draft | 2B | Homer | Bush | MLB |
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| 3 | 22 | 70 | 1997 | Annual Draft | P | Jaret | Wright | MLB |
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| 4 | 22 | 94 | 1997 | Annual Draft | OF | Jason | McDonald | MLB |
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| 6 | 22 | 142 | 1997 | Annual Draft | P | Kirt | Ojala | MLB |
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| 7 | 22 | 166 | 1997 | Annual Draft | C | Angelo | Encarnacion | MLB |
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| 8 | 22 | 190 | 1997 | Annual Draft | OF | Wendell | Magee | MLB |
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| 2 | 14 | 38 | 1996 | Annual Draft | P | Ramiro | Mendoza | MLB |
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| 2 | 18 | 42 | 1996 | Annual Draft | 2B | Ryne | Sandberg | MLB |
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| 3 | 13 | 61 | 1996 | Annual Draft | P | Danny | Patterson | MLB |
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| 4 | 14 | 86 | 1996 | Annual Draft | P | Mike | Holtz | MLB |
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| 5 | 13 | 109 | 1996 | Annual Draft | 2B+ | Andy | Stankiewicz | MLB |
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| 6 | 14 | 134 | 1996 | Annual Draft | P | Dan | Serafini | MLB |
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| 7 | 13 | 157 | 1996 | Annual Draft | 2B+ | Kurt | Stillwell | MLB |
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| 8 | 14 | 182 | 1996 | Annual Draft | OF+ | Brian | Banks | MLB |
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| 9 | 13 | 205 | 1996 | Annual Draft | OF | Brent | Bowers | MLB |
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| 1 | 1 | 1 | 1995 | Inaugural Draft | OF | Barry | Bonds | MLB |
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| 2 | 24 | 48 | 1995 | Inaugural Draft | 3B+ | Vinny | Castilla | MLB |
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| 3 | 1 | 49 | 1995 | Inaugural Draft | OF | Juan | Gonzalez | MLB |
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| 4 | 24 | 96 | 1995 | Inaugural Draft | P | Alex | Fernandez | MLB |
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| 5 | 1 | 97 | 1995 | Inaugural Draft | P | Shane | Reynolds | MLB |
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| 6 | 24 | 144 | 1995 | Inaugural Draft | C | Todd | Hundley | MLB |
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| 7 | 1 | 145 | 1995 | Inaugural Draft | P | Darryl | Kile | MLB |
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| 8 | 24 | 192 | 1995 | Inaugural Draft | 1B+ | David | Segui | MLB |
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| 9 | 1 | 193 | 1995 | Inaugural Draft | P | Jim | Abbott | MLB |
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| 10 | 24 | 240 | 1995 | Inaugural Draft | P | Mike | Jackson | MLB |
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| 11 | 1 | 241 | 1995 | Inaugural Draft | P | Juan | Guzman | MLB |
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| 12 | 24 | 288 | 1995 | Inaugural Draft | 1B | John | Jaha | MLB |
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| 13 | 1 | 289 | 1995 | Inaugural Draft | P | Eric | Plunk | MLB |
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| 14 | 24 | 336 | 1995 | Inaugural Draft | OF | Jim | Eisenreich | MLB |
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| 15 | 1 | 337 | 1995 | Inaugural Draft | 2B | Jeff | Frye | MLB |
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| 16 | 24 | 384 | 1995 | Inaugural Draft | P | Tim | Crabtree | MLB |
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| 17 | 1 | 385 | 1995 | Inaugural Draft | P | Alan | Benes | MLB |
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| 18 | 24 | 432 | 1995 | Inaugural Draft | 3B+ | Mark | Lewis | MLB |
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| 19 | 1 | 433 | 1995 | Inaugural Draft | OF | Rich | Amaral | MLB |
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| 20 | 24 | 480 | 1995 | Inaugural Draft | OF | Todd | Hollandsworth | MLB |
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| 21 | 1 | 481 | 1995 | Inaugural Draft | P | Mike | Williams | MLB |
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| 22 | 24 | 528 | 1995 | Inaugural Draft | C | Carlos | Hernandez | MLB |
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| 23 | 1 | 529 | 1995 | Inaugural Draft | P | John | Frascatore | MLB |
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| 24 | 24 | 576 | 1995 | Inaugural Draft | SS | Benji | Gil | MLB |
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| 25 | 1 | 577 | 1995 | Inaugural Draft | P | Brian | Boehringer | MLB |
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| 26 | 24 | 624 | 1995 | Inaugural Draft | P | Omar | Olivares | MLB |
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| 27 | 1 | 625 | 1995 | Inaugural Draft | P | Gregg | Olson | MLB |
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| 28 | 24 | 672 | 1995 | Inaugural Draft | P | Jim | Bruske | MLB |
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| 29 | 1 | 673 | 1995 | Inaugural Draft | OF+ | Melvin | Nieves | MLB |
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| 30 | 24 | 720 | 1995 | Inaugural Draft | OF | Ozzie | Timmons | MLB |
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| 31 | 1 | 721 | 1995 | Inaugural Draft | C | George | Williams | MLB |
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| 32 | 24 | 768 | 1995 | Inaugural Draft | P | Josias | Manzanillo | MLB |
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| 33 | 1 | 769 | 1995 | Inaugural Draft | OF | Dwight | Smith | MLB |
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| 34 | 24 | 816 | 1995 | Inaugural Draft | 2B+ | Chip | Hale | MLB |
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| 35 | 1 | 817 | 1995 | Inaugural Draft | 2B+ | Scott | Fletcher | MLB |
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| 36 | 24 | 864 | 1995 | Inaugural Draft | P | Clint | Sodowsky | MLB |
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| 37 | 1 | 865 | 1995 | Inaugural Draft | P | Dennis | Springer | MLB |
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| 38 | 24 | 912 | 1995 | Inaugural Draft | 1B+ | Chris | Sabo | MLB |
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| 39 | 1 | 913 | 1995 | Inaugural Draft | P | Tanyon | Sturtze | MLB |
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| 40 | 24 | 960 | 1995 | Inaugural Draft | P | A.J. | Sager | MLB |
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