Top 50 Songs of 1999
| No. | Song | Band | Album | Previous Rank |
| 1 | Otherside | Red Hot Chili Peppers | Californication | 1 |
| 2 | No Shelter | Rage Against the Machine | The Battle of Los Angeles | 2 |
| 3 | Californication | Red Hot Chili Peppers | Californication | 8 |
| 4 | All The Small Things | Blink-182 | Enema of the State | 3 |
| 5 | Run | Collective Soul | Dosage | 5 |
| 6 | Thief | Our Lady Peace | Happiness... Is Not A Fish That You Can Catch | 4 |
| 7 | Broken Chairs | Built to Spill | Keep it like a Secret | N/A |
| 8 | All Star | Smash Mouth | Astro Lounge | 6 |
| 9 | Why I'm Here | Oleander | February Son | 16 |
| 10 | Sour Girl | Stone Temple Pilots | No. 4 | 7 |
| 11 | Never Let You Go | Third Eye Blind | Blue | 18 |
| 12 | All My Friends | Counting Crows | This Desert Life | 17 |
| 13 | Blue | Eiffel 65 | Europop | 13 |
| 14 | We Are | Vertical Horizon | Everything You Want | 22 |
| 15 | 9PM | ATB | Movin' Melodies | 27 |
| 16 | Good Morning Baby | Bic Runga and Dan Wilson | Soundtrack: American Pie | N/A |
| 17 | The Chemicals Between Us | Bush | The Science of Things | 11 |
| 18 | Stranger By the Day | Shades Apart | Eyewitness | 39 |
| 19 | Whats My Age Again? | Blink-182 | Enema of the State | 19 |
| 20 | Take a Picture | Filter | Title of Record | 37 |
| 21 | Else | Built to Spill | Keep it like a Secret | N/A |
| 22 | Drive | Incubus | Make Yourself | 25 |
| 23 | Forgot About Dre | Dr. Dre | 2001 | 20 |
| 24 | Compliment | Collective Soul | Dosage | N/A |
| 25 | You Were Right | Built to Spill | Keep it like a Secret | N/A |
| 26 | Warm Machine | Bush | The Science of Things | 35 |
| 27 | Genie in a Bottle | Christina Aguilera | Christina Aguilera | 40 |
| 28 | Steal my Sunshine | Len | You Can't Stop the Bum Rush | N/A |
| 29 | Everything You Want | Vertical Horizon | Everything You Want | 33 |
| 30 | Uno | Muse | Showbiz | 28 |
| 31 | What The Hell Have I? | Alice in Chains | Nothing Safe | N/A |
| 32 | Scar Tissue | Red Hot Chili Peppers | Californication | 29 |
| 33 | Muscle Museum | Muse | Showbiz | N/A |
| 34 | Higher | Creed | Human Clay | N/A |
| 35 | Beautiful Stranger | Madonna | Soundtrack: Austin Powers 2 | N/A |
| 36 | Bailamos | Enrique Iglesias | Enrique | N/A |
| 37 | Next Year | Foo Fighters | There is Nothing Left to Lose | N/A |
| 38 | Ana's Song | Silverchair | Neon Ballroom | 23 |
| 39 | You Say | Vertical Horizon | Everything You Want | N/A |
| 40 | Died | Alice in Chains | Music Bank | 10 |
| 41 | Better Days | Citizen King | Mobile Estates | N/A |
| 42 | Welcome to the Fold | Filter | Title of Record | N/A |
| 43 | I Need To Know | Marc Anthony | Marc Anthony | N/A |
| 44 | Get Born Again | Alice in Chains | Nothing Safe | N/A |
| 45 | Little Black Backpack | Stroke 9 | Nasty Little Thoughts | N/A |
| 46 | I Got You | Stone Temple Pilots | No. 4 | N/A |
| 47 | Baby One More Time | Britney Spears | ....Baby One More Time | N/A |
| 48 | You Stole The Sun From My Heart | Manic Street Preachers | This Is My Truth Tell Me Yours | 32 |
| 49 | Captain Badass | Songs: Ohia | Axxess & Ace | N/A |
| 50 | Major Leagues | Pavement | Terror Twilight | N/A |
| Updated 02/08/08: Extended from 40 to 50 |