Number one modern rock hits of 1999
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These are the Billboard magazine Modern Rock Tracks number one hits of 1999.
| Issue Date | Song | Artist |
| January 2 | What It's Like | Everlast |
| January 9 | What It's Like | Everlast |
| January 16 | What It's Like | Everlast |
| January 23 | What It's Like | Everlast |
| January 30 | What It's Like | Everlast |
| February 6 | What It's Like | Everlast |
| February 13 | What It's Like | Everlast |
| February 20 | Every Morning | Sugar Ray |
| February 27 | What It's Like | Everlast |
| March 6 | Every Morning | Sugar Ray |
| March 13 | Every Morning | Sugar Ray |
| March 20 | Every Morning | Sugar Ray |
| March 27 | Every Morning | Sugar Ray |
| April 3 | Every Morning | Sugar Ray |
| April 10 | My Own Worst Enemy | Lit |
| April 17 | My Own Worst Enemy | Lit |
| April 24 | My Own Worst Enemy | Lit |
| May 1 | My Own Worst Enemy | Lit |
| May 8 | My Own Worst Enemy | Lit |
| May 15 | My Own Worst Enemy | Lit |
| May 22 | My Own Worst Enemy | Lit |
| May 29 | My Own Worst Enemy | Lit |
| June 5 | My Own Worst Enemy | Lit |
| June 12 | My Own Worst Enemy | Lit |
| June 19 | My Own Worst Enemy | Lit |
| June 26 | Scar Tissue | Red Hot Chili Peppers |
| July 3 | Scar Tissue | Red Hot Chili Peppers |
| July 10 | Scar Tissue | Red Hot Chili Peppers |
| July 17 | Scar Tissue | Red Hot Chili Peppers |
| July 24 | Scar Tissue | Red Hot Chili Peppers |
| July 31 | Scar Tissue | Red Hot Chili Peppers |
| August 7 | Scar Tissue | Red Hot Chili Peppers |
| August 14 | Scar Tissue | Red Hot Chili Peppers |
| August 21 | Scar Tissue | Red Hot Chili Peppers |
| August 28 | Scar Tissue | Red Hot Chili Peppers |
| September 4 | Scar Tissue | Red Hot Chili Peppers |
| September 11 | Scar Tissue | Red Hot Chili Peppers |
| September 18 | Scar Tissue | Red Hot Chili Peppers |
| September 25 | Scar Tissue | Red Hot Chili Peppers |
| October 2 | Scar Tissue | Red Hot Chili Peppers |
| October 9 | Scar Tissue | Red Hot Chili Peppers |
| October 16 | Higher | Creed |
| October 23 | The Chemicals Between Us | Bush |
| October 30 | The Chemicals Between Us | Bush |
| November 6 | Learn to Fly | Foo Fighters |
| November 13 | The Chemicals Between Us | Bush |
| November 20 | The Chemicals Between Us | Bush |
| November 27 | Higher | Creed |
| December 4 | The Chemicals Between Us | Bush |
| December 11 | Higher | Creed |
| December 18 | Re-Arranged | Limp Bizkit |
| December 25 | All the Small Things | Blink-182 |
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