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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