11 selections by the Atlanta Thrashers in the 1999 NHL Entry Draft.
| Year | Pick | Round | Team | Player | Pos | Amateur Club | League | Country |
|---|---|---|---|---|---|---|---|---|
| 1999 | 1 | 1 | ATLAtlanta Thrashers | Patrik Stefan | C | Long Beach Ice Dogs | IHL | CZE |
| 1999 | 30 | 2 | ATLAtlanta Thrashers | Luke Sellars | D | Ottawa 67's | OHL | CAN |
| 1999 | 68 | 3 | ATLAtlanta Thrashers | Zdenek Blatny | LW | Seattle Thunderbirds | WHL | CZE |
| 1999 | 98 | 4 | ATLAtlanta Thrashers | David Kaczowka | LW | Seattle Thunderbirds | WHL | CAN |
| 1999 | 99 | 4 | ATLAtlanta Thrashers | Rob Zepp | G | Plymouth Whalers | OHL | CAN |
| 1999 | 128 | 5 | ATLAtlanta Thrashers | Derek MacKenzie | C | Sudbury Wolves | OHL | CAN |
| 1999 | 159 | 6 | ATLAtlanta Thrashers | Yuri Dobryshkin | RW | Krylja Sovetov | Russia | RUS |
| 1999 | 188 | 7 | ATLAtlanta Thrashers | Stephen Baby | RW | Green Bay Gamblers | USHL | USA |
| 1999 | 217 | 8 | ATLAtlanta Thrashers | Garnet Exelby | D | Saskatoon Blades | WHL | CAN |
| 1999 | 245 | 9 | ATLAtlanta Thrashers | Tommi Santala | C | Jokerit Helsinki | FINLAND | FIN |
| 1999 | 246 | 9 | ATLAtlanta Thrashers | Ray Dilauro | D | St. Lawrence University | NCAA | USA |