# 1999 NAIA Division II men's basketball tournament

The 1999 NAIA Division II men's basketball tournament was the tournament held by the NAIA to determine the national champion of men's college basketball among its Division II members in the United States and Canada for the 1998–99 basketball season.
Top-seeded Cornerstone defeated two-time defending champions Bethel (IN) in the championship game, 113–109 after one overtime period, to claim the Golden Eagles' first NAIA national title.
The tournament was played at the Idaho Center at Northwest Nazarene University in Nampa, Idaho.

## Qualification

The tournament field remained fixed at thirty-two teams, and the top sixteen teams were seeded.
The tournament continued to utilize a single-elimination format.

## Bracket

| First round | First round | First round | Second round | Second round | Second round | Quarterfinals | Quarterfinals | Quarterfinals | | Semifinals | Semifinals | Semifinals | | National championship | National championship | National championship |
| 1 | Cornerstone | 88 | | | | | | | | | | | | | | |
| | Doane | 72 | | | | | | | | | | | | | | |
| | Doane | 72 | 1 | Cornerstone | 107 | | | | | | | | | | | |
| | | | | Western Oregon | 92 | | | | | | | | | | | |
| | Western Oregon | 91 | | Western Oregon | 92 | | | | | | | | | | | |
| 16 | Jamestown | 63 | | | | | | | | | | | | | | |
| 16 | Jamestown | 63 | | | | 1 | Cornerstone | 72 | | | | | | | | |
| | | | | | | | Huron | 70 | | | | | | | | |
| 9 | Mount Vernon Nazarene | 87 | | | | | | | | Huron | 70 | | | | | | | | |
| | Huron | 97 | | | | | | | | | | | | | | |
| | Huron | 97 | | Huron | 81 | | | | | | | | | | | |
| | | | 8 | Albertson | 70 | | | | | | | | | | | |
| | Bethany (KS) | 73 | 8 | Albertson | 70 | | | | | | | | | | | |
| 8 | Albertson | 78 | | | | | | | | | | | | | | |
| 8 | Albertson | 78 | | | | | | | | 1 | Cornerstone | 100 | | | | |
| | | | | | | | | | | 13 | Berea | 85 | | | | |
| 5 | MidAmerica Nazarene | 68 | | | | | | | | | | | 13 | Berea | 85 | | | | |
| | Viterbo | 76 | | | | | | | | | | | | | | |
| | Viterbo | 76 | | Viterbo | 91 | | | | | | | | | | | |
| | | | 12 | Cal State Hayward | 82 | | | | | | | | | | | |
| | Husson | 78 | 12 | Cal State Hayward | 82 | | | | | | | | | | | |
| 12 | Cal State Hayward | 94 | | | | | | | | | | | | | | |
| 12 | Cal State Hayward | 94 | | | | | Viterbo | 74 | | | | | | | | |
| | | | | | | 13 | Berea | 85 | | | | | | | | |
| 13 | Berea | 86 | | | | | | | 13 | Berea | 85 | | | | | | | | |
| | Briar Cliff | 76 | | | | | | | | | | | | | | |
| | Briar Cliff | 76 | 13 | Berea | 94 | | | | | | | | | | | |
| | | | 4 | Milligan | 84 | | | | | | | | | | | |
| | Green Mountain | 75 | 4 | Milligan | 84 | | | | | | | | | | | |
| 4 | Milligan | 94 | | | | | | | | | | | | | | |
| 4 | Milligan | 94 | | | | | | | | | | | | 1 | Cornerstone | 113* |
| | | | | | | | | | | | | | | 2 | Bethel (IN) | 109 |
| 3 | Southern Oregon | 87 | | | | | | | | | | | | | | | 2 | Bethel (IN) | 109 |
| | Bluefield (VA) | 88 | | | | | | | | | | | | | | |
| | Bluefield (VA) | 88 | | Bluefield (VA) | 71 | | | | | | | | | | | |
| | | | | Mount Senario | 85 | | | | | | | | | | | |
| | Mount Senario | 100 | | Mount Senario | 85 | | | | | | | | | | | |
| 14 | Saint Joseph's (ME) | 72 | | | | | | | | | | | | | | |
| 14 | Saint Joseph's (ME) | 72 | | | | | Mount Senario | 77 | | | | | | | | |
| | | | | | | 11 | Northwestern (IA) | 73 | | | | | | | | |
| 11 | Northwestern (IA) | 72 | | | | | | | 11 | Northwestern (IA) | 73 | | | | | | | | |
| | Evangel | 64 | | | | | | | | | | | | | | |
| | Evangel | 64 | 11 | Northwestern (IA) | 67 | | | | | | | | | | | |
| | | | 6 | Siena Heights | 53 | | | | | | | | | | | |
| | Caldwell | 68 | 6 | Siena Heights | 53 | | | | | | | | | | | |
| 6 | Siena Heights | 92 | | | | | | | | | | | | | | |
| 6 | Siena Heights | 92 | | | | | | | | | Mount Senario | 72 | | | | |
| | | | | | | | | | | 2 | Bethel (IN) | 90 | | | | |
| 7 | Embry–Riddle (FL) | 97 | | | | | | | | | | | 2 | Bethel (IN) | 90 | | | | |
| | Bellevue | 73 | | | | | | | | | | | | | | |
| | Bellevue | 73 | 7 | Embry–Riddle (FL) | 72 | | | | | | | | | | | |
| | | | 10 | Black Hills State | 78 | | | | | | | | | | | |
| | Holy Family | 76 | 10 | Black Hills State | 78 | | | | | | | | | | | |
| 10 | Black Hills State | 100 | | | | | | | | | | | | | | |
| 10 | Black Hills State | 100 | | | | 10 | Black Hills State | 72 | | | | | | | | |
| | | | | | | 2 | Bethel (IN) | 89 | | | | | | | | |
| 15 | Cardinal Stritch | 95 | | | | | | | 2 | Bethel (IN) | 89 | | | | | | | | |
| | Cal State Monterey Bay | 67 | | | | | | | | | | | | | | |
| | Cal State Monterey Bay | 67 | 15 | Cardinal Stritch | 91 | | | | | | | | | | | |
| | | | 2 | Bethel (IN) | 111 | | | | | | | | | | | |
| | Northwest Nazarene | 90 | 2 | Bethel (IN) | 111 | | | | | | | | | | | |
| 2 | Bethel (IN) | 96 | | | | | | | | | | | | | | |