The Men's 400 metres event at the 2006 IAAF World Indoor Championships was held on March 10–12.
| width=200 bgcolor=gold | Gold | width=200 bgcolor=silver | Silver | width=200 bgcolor=CC9966 | Bronze |
| Alleyne Francique | California Molefe | Chris Brown |
First 2 of each heat (Q) and the next 2 fastest (q) qualified for the semifinals.
| Rank | Heat | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|---|
| 1 | 1 | 45.74 | Q, WL, NR | |||
| 2 | 1 | 46.29 | Q | |||
| 3 | 5 | 46.37 | Q | |||
| 4 | 3 | 46.64 | Q | |||
| 5 | 4 | 46.67 | Q | |||
| 6 | 5 | 46.68 | Q | |||
| 7 | 3 | 46.69 | Q | |||
| 8 | 2 | 46.79 | Q | |||
| 9 | 4 | 46.80 | Q | |||
| 10 | 2 | 46.88 | Q | |||
| 11 | 3 | 47.00 | q | |||
| 12 | 2 | 47.02 | q | |||
| 13 | 1 | 47.13 | ||||
| 14 | 4 | 47.32 | PB | |||
| 15 | 4 | 47.33 | SB | |||
| 16 | 1 | 47.36 | ||||
| 17 | 5 | 47.38 | ||||
| 18 | 4 | 47.50 | NR | |||
| 19 | 1 | 47.61 | SB | |||
| 20 | 5 | 48.19 | ||||
| 21 | 2 | 48.26 | ||||
| 22 | 3 | 48.45 | NR | |||
| 23 | 4 | 48.52 | ||||
| 24 | 1 | 49.95 | NR | |||
| 25 | 5 | 54.80 | NR | |||
| 2 | ||||||
| 3 | ||||||
| 5 |
First 3 of each semifinal qualified directly (Q) for the final.
| Rank | Heat | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|---|
| 1 | 1 | 45.86 | Q | |||
| 2 | 1 | 46.02 | Q | |||
| 3 | 2 | 46.10 | Q | |||
| 4 | 1 | 46.22 | Q | |||
| 5 | 2 | 46.23 | Q, SB | |||
| 6 | 2 | 46.44 | Q | |||
| 7 | 1 | 46.61 | ||||
| 8 | 1 | 46.67 | ||||
| 9 | 2 | 46.97 | ||||
| 10 | 1 | 47.11 | ||||
| 10 | 2 | 47.11 | ||||
| 10 | 2 | 47.11 |
| Rank | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|
| 45.54 | SB | ||||
| 45.75 | |||||
| 45.78 | NR | ||||
| 4 | 45.93 | SB | |||
| 5 | 46.15 | SB | |||
| 6 | 47.33 |