Hot 100 number-one hits of 1999 (USA)
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This is a list of the U.S. Billboard magazine Hot 100 number-ones of 1999.
| Issue Date | Song | Artist |
| January 2 | I'm Your Angel | R. Kelly and Céline Dion |
| January 9 | I'm Your Angel | R. Kelly and Céline Dion |
| January 16 | Have You Ever? | Brandy |
| January 23 | Have You Ever? | Brandy |
| January 30 | ...Baby One More Time | Britney Spears |
| February 6 | ...Baby One More Time | Britney Spears |
| February 13 | Angel of Mine | Monica |
| February 20 | Angel of Mine | Monica |
| February 27 | Angel of Mine | Monica |
| March 6 | Angel of Mine | Monica |
| March 13 | Believe | Cher |
| March 20 | Believe | Cher |
| March 27 | Believe | Cher |
| April 3 | Believe | Cher |
| April 10 | No Scrubs | TLC |
| April 17 | No Scrubs | TLC |
| April 24 | No Scrubs | TLC |
| May 1 | No Scrubs | TLC |
| May 8 | Livin' la Vida Loca | Ricky Martin |
| May 15 | Livin' la Vida Loca | Ricky Martin |
| May 22 | Livin' la Vida Loca | Ricky Martin |
| May 29 | Livin' la Vida Loca | Ricky Martin |
| June 5 | Livin' la Vida Loca | Ricky Martin |
| June 12 | If You Had My Love | Jennifer Lopez |
| June 19 | If You Had My Love | Jennifer Lopez |
| June 26 | If You Had My Love | Jennifer Lopez |
| July 3 | If You Had My Love | Jennifer Lopez |
| July 10 | If You Had My Love | Jennifer Lopez |
| July 17 | Bills, Bills, Bills | Destiny's Child |
| July 24 | Wild Wild West | Will Smith featuring Dru Hill and Kool Moe Dee |
| July 31 | Genie in a Bottle | Christina Aguilera |
| August 7 | Genie in a Bottle | Christina Aguilera |
| August 14 | Genie in a Bottle | Christina Aguilera |
| August 21 | Genie in a Bottle | Christina Aguilera |
| August 28 | Genie in a Bottle | Christina Aguilera |
| September 4 | Bailamos | Enrique Iglesias |
| September 11 | Bailamos | Enrique Iglesias |
| September 18 | Unpretty | TLC |
| September 25 | Unpretty | TLC |
| October 2 | Unpretty | TLC |
| October 9 | Heartbreaker | Mariah Carey featuring Jay-Z |
| October 16 | Heartbreaker | Mariah Carey featuring Jay-Z |
| October 23 | Smooth | Santana featuring Rob Thomas |
| October 30 | Smooth | Santana featuring Rob Thomas |
| November 6 | Smooth | Santana featuring Rob Thomas |
| November 13 | Smooth | Santana featuring Rob Thomas |
| November 20 | Smooth | Santana featuring Rob Thomas |
| November 27 | Smooth | Santana featuring Rob Thomas |
| December 4 | Smooth | Santana featuring Rob Thomas |
| December 11 | Smooth | Santana featuring Rob Thomas |
| December 18 | Smooth | Santana featuring Rob Thomas |
| December 25 | Smooth | Santana featuring Rob Thomas |
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