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| First Round Draft Pick History |
| 1 | 7 | 7 | 1999 | Annual Draft | P | Charles | Nagy | MLB |
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| 1 | 4 | 4 | 1998 | Annual Draft | P | Dennis | Martinez | MLB |
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| 1 | 5 | 5 | 1997 | Annual Draft | P | John | Smiley | MLB |
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| Complete Draft History |
| 1 | 7 | 7 | 1999 | Annual Draft | P | Charles | Nagy | MLB |
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| 2 | 6 | 18 | 1999 | Annual Draft | OF | Tony | Phillips | MLB |
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| 3 | 7 | 31 | 1999 | Annual Draft | 3B | John | Valentin | MLB |
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| 4 | 6 | 42 | 1999 | Annual Draft | P | Terry | Mulholland | MLB |
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| 5 | 7 | 55 | 1999 | Annual Draft | SS | Walt | Weiss | MLB |
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| 6 | 6 | 66 | 1999 | Annual Draft | P | Ken | Hill | MLB |
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| 7 | 7 | 79 | 1999 | Annual Draft | OF | Jeromy | Burnitz | MLB |
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| 8 | 6 | 90 | 1999 | Annual Draft | OF+ | Matt | Stairs | MLB |
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| 9 | 7 | 103 | 1999 | Annual Draft | P | Jose | Mesa | MLB |
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| 10 | 6 | 114 | 1999 | Annual Draft | 3B+ | Bill | Mueller | MLB |
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| 11 | 7 | 127 | 1999 | Annual Draft | P | Justin | Thompson | MLB |
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| 12 | 6 | 138 | 1999 | Annual Draft | OF | Troy | O'Leary | MLB |
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| 1 | 4 | 4 | 1998 | Annual Draft | P | Dennis | Martinez | MLB |
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| 2 | 4 | 20 | 1998 | Annual Draft | C+ | Chris | Hoiles | MLB |
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| 2 | 15 | 31 | 1998 | Annual Draft | P | Scott | Radinsky | MLB |
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| 3 | 4 | 36 | 1998 | Annual Draft | C+ | Jim | Leyritz | MLB |
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| 4 | 4 | 52 | 1998 | Annual Draft | OF+ | Jim | Eisenreich | MLB |
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| 5 | 4 | 68 | 1998 | Annual Draft | OF | Glenallen | Hill | MLB |
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| 6 | 4 | 84 | 1998 | Annual Draft | P | Kerry | Ligtenberg | MLB |
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| 1 | 5 | 5 | 1997 | Annual Draft | P | John | Smiley | MLB |
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| 2 | 4 | 20 | 1997 | Annual Draft | OF | Danny | Tartabull | MLB |
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| 3 | 4 | 36 | 1997 | Annual Draft | P | Tony | Fossas | MLB |
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| 3 | 5 | 37 | 1997 | Annual Draft | P | Mike | James | MLB |
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| 4 | 4 | 52 | 1997 | Annual Draft | OF | Jon | Nunnally | MLB |
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| 5 | 5 | 69 | 1997 | Annual Draft | 3B+ | Dave | Hansen | MLB |
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| 8 | 4 | 116 | 1997 | Annual Draft | | SKIPPED | PICK | MLB |
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| 2 | 10 | 26 | 1996 | Annual Draft | P | Terrell | Wade | MLB |
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| 3 | 3 | 35 | 1996 | Annual Draft | 2B+ | Tony | Batista | MLB |
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| 3 | 13 | 45 | 1996 | Annual Draft | P | Gregg | Olson | MLB |
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| 6 | 10 | 90 | 1996 | Annual Draft | OF | Jeromy | Burnitz | MLB |
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| 7 | 13 | 109 | 1996 | Annual Draft | OF | John | Cangelosi | MLB |
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| 8 | 10 | 122 | 1996 | Annual Draft | P | Larry | Casian | MLB |
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| 9 | 13 | 141 | 1996 | Annual Draft | OF | Curtis | Pride | MLB |
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