| 1 | 1999 | Mule Variations | Tom Waits | Album | 4.6 | 9 |
| 2 | 1999 | Electric Honey | Luscious Jackson | Album | 4 | 4 |
| 3 | 1999 | Summerteeth | Wilco | Album | 4.5 | 8 |
| 4 | 1999 | Worried | Asie Payton | Album | | 1 |
| 5 | 1999 | In Session | Albert King with Stevie Ray Vaughan | Album + Live | 4.65 | 9 |
| 6 | 1999 | Midnite Vultures | Beck | Album | 4 | 13 |
| 7 | 1999 | When the Pawn Hits the Conflicts He Thinks Like a King What He Knows Throws the Blows When He Goes to the Fight and He’ll Win the Whole Thing ’Fore He Enters the Ring There’s No Body to Batter When Your Mind Is Your Might So When You Go Solo, You Hold Your Own Hand and Remember That Depth Is the Greatest of Heights and If You Know Where You Stand, Then You Know Where to Land and If You Fall It Won’t Matter, Cuz You’ll Know That You’re Right | Fiona Apple | Album | 4.45 | 18 |
| 8 | 1999 | Echo | Tom Petty and the Heartbreakers | Album | 3 | 9 |
| 9 | 1999 | Take Your Shoes Off | The Robert Cray Band | Album | | 1 |
| 10 | 1999 | In Reverse | Matthew Sweet | Album | | 4 |
| 11 | 1999 | Go Simpsonic With the Simpsons: More Original Music From the Television Series | The Simpsons | Album + Soundtrack | | 5 |
| 12 | 1999 | Do the Collapse | Guided by Voices | Album | 5 | 8 |
| 13 | 1999 | A Far Cry From Dead | Townes Van Zandt | Album + Compilation | | 1 |
