The men's 800 metres event at the 1999 IAAF World Indoor Championships was held on March 5–7.
| Gold | Silver | Bronze | |
| Johan Botha | Wilson Kipketer | Nico Motchebon |
First 2 of each heat (Q) and next 8 fastest (q) qualified for the semifinals.
| Rank | Heat | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|---|
| 1 | 1 | 1:48.00 | Q | |||
| 2 | 5 | 1:48.07 | Q | |||
| 3 | 5 | 1:48.10 | Q | |||
| 4 | 5 | 1:48.13 | q | |||
| 5 | 2 | 1:48.31 | Q | |||
| 6 | 5 | 1:48.32 | q, SB | |||
| 7 | 2 | 1:48.33 | Q | |||
| 8 | 1 | 1:48.34 | Q | |||
| 9 | 1 | 1:48.46 | q | |||
| 10 | 2 | 1:48.61 | q | |||
| 11 | 1 | 1:48.68 | q, PB | |||
| 12 | 5 | 1:49.03 | q | |||
| 13 | 2 | 1:49.08 | q | |||
| 14 | 1 | 1:49.11 | q | |||
| 15 | 4 | 1:49.29 | Q | |||
| 16 | 4 | 1:49.38 | Q | |||
| 17 | 4 | 1:49.64 | ||||
| 18 | 4 | 1:49.81 | ||||
| 19 | 4 | 1:50.37 | ||||
| 20 | 2 | 1:50.94 | ||||
| 21 | 3 | 1:52.26 | Q | |||
| 22 | 3 | 1:52.38 | Q | |||
| 23 | 3 | 1:52.43 | ||||
| 24 | 3 | 1:52.48 | ||||
| 25 | 3 | 1:53.09 | ||||
| 26 | 2 | 1:58.17 |
First 2 of each semifinal qualified directly (Q) for the final.
| Rank | Heat | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|---|
| 1 | 2 | 1:46.65 | Q | |||
| 2 | 2 | 1:46.76 | Q | |||
| 3 | 2 | 1:46.80 | PB | |||
| 4 | 1 | 1:47.05 | Q | |||
| 5 | 2 | 1:47.45 | SB | |||
| 6 | 1 | 1:47.54 | Q | |||
| 7 | 1 | 1:47.58 | ||||
| 8 | 1 | 1:48.17 | ||||
| 9 | 2 | 1:48.35 | ||||
| 10 | 1 | 1:48.61 | ||||
| 11 | 3 | 1:48.74 | Q | |||
| 12 | 3 | 1:48.85 | Q | |||
| 13 | 3 | 1:48.88 | ||||
| 14 | 2 | 1:49.18 | ||||
| 15 | 3 | 1:49.38 | ||||
| 16 | 3 | 1:49.57 | ||||
| 17 | 3 | 1:50.18 | ||||
| 1 |
| Rank | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|
| 1:45.47 | |||||
| 1:45.49 | |||||
| 1:45.74 | |||||
| 4 | 1:46.47 | NR | |||
| 5 | 1:47.77 | ||||
| 6 | 1:47.79 |