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| First Round Draft Pick History |
| 1 | 16 | 16 | 2009 | Annual Draft | 3B | Willy | Aybar | MLB |
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| 1 | 25 | 25 | 2008 | Inaugural Draft | C | Joe | Mauer | MLB |
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| Complete Draft History |
| 1 | 16 | 16 | 2009 | Annual Draft | 3B | Willy | Aybar | MLB |
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| 2 | 15 | 43 | 2009 | Annual Draft | 1B | David | Cooper | MIN |
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| 3 | 16 | 72 | 2009 | Annual Draft | SS | Carlos | Rivero | MIN |
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| 4 | 15 | 99 | 2009 | Annual Draft | SS | Niko | Vasquez | MIN |
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| 5 | 16 | 128 | 2009 | Annual Draft | SP | Jordan | Lyles | MIN |
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| 6 | 15 | 155 | 2009 | Annual Draft | SP | Tyler | Sample | MIN |
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| 7 | 16 | 184 | 2009 | Annual Draft | SP | Albert | Suarez | MIN |
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| 10 | 5 | 257 | 2009 | Annual Draft | SP | Oliver | Drake | MIN |
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| 10 | 15 | 267 | 2009 | Annual Draft | RP | Kanekoa | Texeira | MIN |
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| 11 | 16 | 296 | 2009 | Annual Draft | SS | Jonathan | Barrios | OS |
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| 12 | 15 | 323 | 2009 | Annual Draft | SP | Daniel | Thomas | MIN |
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| 13 | 16 | 352 | 2009 | Annual Draft | OF | Rashun | Dixon | MIN |
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| 14 | 15 | 379 | 2009 | Annual Draft | 1B | Rhyne | Hughes | MIN |
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| 15 | 16 | 408 | 2009 | Annual Draft | SS | Brian | Friday | MIN |
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| 1 | 25 | 25 | 2008 | Inaugural Draft | C | Joe | Mauer | MLB |
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| 2 | 4 | 32 | 2008 | Inaugural Draft | 2B | Howie | Kendrick | MLB |
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| 3 | 25 | 81 | 2008 | Inaugural Draft | OF | Alex | Rios | MLB |
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| 4 | 4 | 88 | 2008 | Inaugural Draft | 3B | Alex | Gordon | MLB |
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| 5 | 25 | 137 | 2008 | Inaugural Draft | OF | Hideki | Matsui | MLB |
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| 6 | 4 | 144 | 2008 | Inaugural Draft | SP | Ubaldo | Jimenez | MLB |
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| 7 | 25 | 193 | 2008 | Inaugural Draft | SP | Boof | Bonser | MLB |
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| 8 | 4 | 200 | 2008 | Inaugural Draft | SP | Shaun | Marcum | MLB |
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| 9 | 25 | 249 | 2008 | Inaugural Draft | SP | Doug | Davis | MLB |
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| 10 | 4 | 256 | 2008 | Inaugural Draft | SP | Lenny | DiNardo | MLB |
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| 11 | 25 | 305 | 2008 | Inaugural Draft | SS | David | Eckstein | MLB |
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| 12 | 4 | 312 | 2008 | Inaugural Draft | OF | Willy | Taveras | MLB |
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| 13 | 25 | 361 | 2008 | Inaugural Draft | 3B | Maicer | Izturis | MLB |
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| 14 | 4 | 368 | 2008 | Inaugural Draft | 1B | Dmitri | Young | MLB |
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| 15 | 25 | 417 | 2008 | Inaugural Draft | OF | Ryan | Spilborghs | MLB |
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| 16 | 4 | 424 | 2008 | Inaugural Draft | 2B | Jose | Vidro | MLB |
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| 17 | 25 | 473 | 2008 | Inaugural Draft | RP | Jimmy | Gobble | MLB |
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| 18 | 4 | 480 | 2008 | Inaugural Draft | RP | Jamie | Walker | MLB |
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| 19 | 25 | 529 | 2008 | Inaugural Draft | C | Matt | Treanor | MLB |
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| 20 | 4 | 536 | 2008 | Inaugural Draft | SP | Tim | Redding | MLB |
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| 21 | 25 | 585 | 2008 | Inaugural Draft | OF | Reed | Johnson | MLB |
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| 22 | 4 | 592 | 2008 | Inaugural Draft | OF | Delwyn | Young | MLB |
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| 23 | 25 | 641 | 2008 | Inaugural Draft | SP | Dustin | Nippert | MLB |
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| 24 | 4 | 648 | 2008 | Inaugural Draft | SP | Steve | Trachsel | MLB |
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| 25 | 25 | 697 | 2008 | Inaugural Draft | SP | Odalis | Perez | MLB |
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| 26 | 4 | 704 | 2008 | Inaugural Draft | SP | Kip | Wells | MLB |
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| 27 | 25 | 753 | 2008 | Inaugural Draft | RP | Todd | Wellemeyer | MLB |
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| 28 | 4 | 760 | 2008 | Inaugural Draft | RP | Brett | Tomko | MLB |
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| 29 | 25 | 809 | 2008 | Inaugural Draft | SP | Ryan | Feierabend | MLB |
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| 30 | 4 | 816 | 2008 | Inaugural Draft | SP | Anthony | Lerew | MLB |
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| 31 | 25 | 865 | 2008 | Inaugural Draft | SP | Angel | Guzman | MLB |
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| 33 | 25 | 921 | 2008 | Inaugural Draft | RP | Chad | Paronto | MLB |
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| 34 | 4 | 928 | 2008 | Inaugural Draft | RP | Tyler J. | Johnson | MLB |
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| 35 | 25 | 977 | 2008 | Inaugural Draft | RP | Matt | Wise | MLB |
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| 36 | 4 | 984 | 2008 | Inaugural Draft | C | J.R. | House | MLB |
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| 37 | 25 | 1033 | 2008 | Inaugural Draft | C | Jason L. | Phillips | MLB |
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| 40 | 4 | 1096 | 2008 | Inaugural Draft | 3B | Vinny | Rottino | MLB |
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| 41 | 25 | 1145 | 2008 | Inaugural Draft | OF | Laynce | Nix | MLB |
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| 43 | 25 | 1201 | 2008 | Inaugural Draft | 1B | Mark | Sweeney | MLB |
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| 44 | 4 | 1208 | 2008 | Inaugural Draft | SS | Cody | Ransom | MLB |
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| 45 | 25 | 1257 | 2008 | Inaugural Draft | RP | David | Aardsma | MLB |
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| 46 | 4 | 1264 | 2008 | Inaugural Draft | RP | Trever | Miller | MLB |
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| 47 | 25 | 1313 | 2008 | Inaugural Draft | RP | Andrew | Sisco | MLB |
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| 48 | 4 | 1320 | 2008 | Inaugural Draft | RP | Tom | Martin | MLB |
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| 50 | 4 | 1376 | 2008 | Inaugural Draft | OF | Justin | Huber | MLB |
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| 51 | 25 | 1425 | 2008 | Inaugural Draft | RP | Juan P. | Perez | MLB |
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| 52 | 4 | 1432 | 2008 | Inaugural Draft | OF | John-Ford | Griffin | MLB |
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| 53 | 25 | 1481 | 2008 | Inaugural Draft | RP | Joe | Bisenius | MLB |
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| 56 | 4 | 1544 | 2008 | Inaugural Draft | RP | Mike | Zagurski | MLB |
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