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| First Round Draft Pick History |
| 1 | 6 | 6 | 2013 | Annual Draft | SP | Kyle | Zimmer | MIN |
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| 1 | 6 | 6 | 2012 | Annual Draft | SP | Brad | Peacock | MLB |
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| Complete Draft History |
| 1 | 6 | 6 | 2013 | Annual Draft | SP | Kyle | Zimmer | MIN |
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| 2 | 6 | 34 | 2013 | Annual Draft | RP | Nick | Maronde | MLB |
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| 2 | 27 | 55 | 2013 | Annual Draft | OF | Daniel | Nava | MLB |
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| 3 | 6 | 62 | 2013 | Annual Draft | OF | Elian | Herrera | MLB |
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| 3 | 19 | 75 | 2013 | Annual Draft | SP | Ben | Sheets | MLB |
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| 4 | 6 | 90 | 2013 | Annual Draft | RP | Cody | Allen | MLB |
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| 6 | 19 | 159 | 2013 | Annual Draft | SP | Tom | Koehler | MLB |
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| 7 | 6 | 174 | 2013 | Annual Draft | SP | Andrew | Werner | MLB |
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| 7 | 13 | 181 | 2013 | Annual Draft | SP | Luis | Mateo | MIN |
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| 8 | 6 | 202 | 2013 | Annual Draft | OF | Andrew | Brown | MLB |
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| 9 | 6 | 230 | 2013 | Annual Draft | OF | Brandon | Barnes | MLB |
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| 11 | 6 | 286 | 2013 | Annual Draft | 2B | Gioskar | Amaya | MIN |
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| 1 | 6 | 6 | 2012 | Annual Draft | SP | Brad | Peacock | MLB |
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| 2 | 6 | 34 | 2012 | Annual Draft | SP | Justin | Nicolino | MIN |
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| 2 | 25 | 53 | 2012 | Annual Draft | SP | Daniel | Corcino | MIN |
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| 3 | 6 | 62 | 2012 | Annual Draft | SP | Jed | Bradley | MIN |
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| 4 | 6 | 90 | 2012 | Annual Draft | OF | Joc | Pederson | MIN |
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| 5 | 6 | 118 | 2012 | Annual Draft | OF | Domingo | Santana | MIN |
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| 5 | 24 | 136 | 2012 | Annual Draft | C | Austin | Hedges | MIN |
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| 6 | 6 | 146 | 2012 | Annual Draft | SS | Jonathan | Villar | MIN |
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| 6 | 28 | 168 | 2012 | Annual Draft | SP | Tyler | Thornburg | MIN |
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| 7 | 6 | 174 | 2012 | Annual Draft | SP | Paul | Clemens | MIN |
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| 7 | 28 | 196 | 2012 | Annual Draft | 3B | Brandon | Drury | MIN |
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| 8 | 6 | 202 | 2012 | Annual Draft | 3B | Maikel | Franco | MIN |
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| 9 | 6 | 230 | 2012 | Annual Draft | SP | Parker | Markel | MIN |
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| 10 | 6 | 258 | 2012 | Annual Draft | OF | Ravel | Santana | MIN |
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| 11 | 6 | 286 | 2012 | Annual Draft | RP | Junichi | Tazawa | MLB |
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| 12 | 6 | 314 | 2012 | Annual Draft | OF | Brandon | Jacobs | MIN |
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| 13 | 6 | 342 | 2012 | Annual Draft | RP | Andrew | Carignan | MLB |
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| 14 | 6 | 370 | 2012 | Annual Draft | RP | George | Kontos | MLB |
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| 15 | 6 | 398 | 2012 | Annual Draft | RP | Kevin | Whelan | MLB |
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