brown #
= weekly rock chart peak
blue #
= pop chart peak
| 1 | Smooth | 10 | 1 | Sep 1999 |  |
| Santana Featuring Rob Thomas |
| 2 | Believe | 1 | Jan 1999 | |
| Cher |
| 3 | Kiss Me | 1 | Apr 1999 | |
| Sixpence None The Richer |
| 4 | Livin' La Vida Loca | 1 | May 1999 | |
| Ricky Martin |
| 5 | Every Morning | 1 | 1 | Feb 1999 | |
| Sugar Ray |
| 6 | I Want It That Way | 1 | May 1999 | |
| Backstreet Boys |
| 7 | The Hardest Thing | 1 | Apr 1999 | |
| 98 Degrees |
| 8 | No Scrubs | 1 | Mar 1999 | |
| TLC |
| 9 | What A Girl Wants | 1 | Dec 1999 | |
| Christina Aguilera |
| 10 | All Star | 1 | 1 | Jul 1999 | |
| Smash Mouth |
| 11 | I Knew I Loved You | 1 | Nov 1999 | |
| Savage Garden |
| 12 | If You Had My Love | 1 | May 1999 | |
| Jennifer Lopez |
| 13 | Music Of My Heart | 1 | Aug 1999 | |
| 'NSYNC & Gloria Estefan |
| 14 | Genie In A Bottle | 1 | Jul 1999 | |
| Christina Aguilera |
| 15 | Angel Of Mine | 1 | Feb 1999 | |
| Monica |
| 16 | Larger Than Life | 2 | Sep 1999 | |
| Backstreet Boys |
| 17 | Pretty Fly (For A White Guy) | 1 | 1 | Jan 1999 | |
| The Offspring |
| 18 | Angel | 1 | Feb 1999 | |
| Sarah McLachlan |
| 19 | I Need To Know | 2 | Oct 1999 | |
| Marc Anthony |
| 20 | All I Have To Give | 2 | Jan 1999 | |
| Backstreet Boys |
| 21 | Unpretty | 1 | Sep 1999 | |
| TLC |
| 22 | Bring It All To Me | 2 | Dec 1999 | |
| Blaque Featuring JC Chasez |
| 23 | Back At One | 1 | Oct 1999 | |
| Brian McKnight |
| 24 | I Wanna Love You Forever | 1 | Nov 1999 | |
| Jessica Simpson |
| 25 | Heartbreaker | 1 | Oct 1999 | |
| Mariah Carey Featuring Jay-Z |