2006 Horizon League baseball tournament
The 2006 Horizon League baseball tournament took place from May 25 through 28, near the close of the 2006 NCAA Division I baseball season. All six of the league's teams met in the double-elimination tournament held at Nischwitz Stadium on the campus of Wright State in Dayton, OH. Third seeded won their second Horizon League Championship and earned the conference's automatic bid to the 2006 NCAA Division I baseball tournament.
Seeding and format
The league's teams are seeded one through six based on winning percentage, using conference games only. The top two seeds receive a single bye in the double-elimination format.| Team | W | L | PCT | GB | Seed |
| 22 | 7 | — | 1 | ||
| 18 | 12 | 4.5 | 2 | ||
| 17 | 13 | 5.5 | 3 | ||
| 16 | 13 | 6 | 4 | ||
| 9 | 21 | 13.5 | 5 | ||
| 6 | 22 | 15.5 | 6 |
All-Tournament Team
The following players were named to the All-Tournament Team.| Name | School |
| Robert Barrett | Wright State |
| Brian Deter | Butler |
| Aaron Garcia | Wright State |
| Jeremy Hamilton | Wright State |
| Ross Oeder | Wright State |
| Jeff Brown | Butler |
| Stephen Gill | Butler |
| Amin Abusaleh | Wright State |
| Ted Rosinski | UIC |
| Justin Wilson | Wright State |
| Rob Brockel | Milwaukee |