Number one modern rock hits of 2006
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These are the Billboard magazine Modern Rock Tracks number one hits of 2006.
| Issue Date | Song | Artist |
| January 7 | "DOA" | Foo Fighters |
| January 14 | "DOA" | Foo Fighters |
| January 21 | "Hypnotize" | System of a Down |
| January 28 | "Perfect Situation" | Weezer |
| February 4 | "Perfect Situation" | Weezer |
| February 11 | "Perfect Situation" | Weezer |
| February 18 | "Perfect Situation" | Weezer |
| February 25 | "Wasteland" | 10 Years |
| March 4 | "Every Day Is Exactly the Same" | Nine Inch Nails |
| March 11 | "Every Day Is Exactly the Same" | Nine Inch Nails |
| March 18 | "Every Day Is Exactly the Same" | Nine Inch Nails |
| March 25 | "Every Day Is Exactly the Same" | Nine Inch Nails |
| April 1 | "World Wide Suicide" | Pearl Jam |
| April 8 | "World Wide Suicide" | Pearl Jam |
| April 15 | "World Wide Suicide" | Pearl Jam |
| April 22 | "Dani California" | Red Hot Chili Peppers |
| April 29 | "Dani California" | Red Hot Chili Peppers |
| May 6 | "Dani California" | Red Hot Chili Peppers |
| May 13 | "Dani California" | Red Hot Chili Peppers |
| May 20 | "Dani California" | Red Hot Chili Peppers |
| May 27 | "Dani California" | Red Hot Chili Peppers |
| June 3 | "Dani California" | Red Hot Chili Peppers |
| June 10 | "Dani California" | Red Hot Chili Peppers |
| June 17 | "Dani California" | Red Hot Chili Peppers |
| June 24 | "Dani California" | Red Hot Chili Peppers |
| July 1 | "Dani California" | Red Hot Chili Peppers |
| July 8 | "Dani California" | Red Hot Chili Peppers |
| July 15 | "Dani California" | Red Hot Chili Peppers |
| July 22 | "Dani California" | Red Hot Chili Peppers |
| July 29 | "Steady, As She Goes" | The Raconteurs |
| August 5 | "Miss Murder" | AFI |
| August 12 | "Miss Murder" | AFI |
| August 19 | "Miss Murder" | AFI |
| August 26 | "Miss Murder" | AFI |
| September 2 | "Miss Murder" | AFI |
| September 9 | "Animal I Have Become" | Three Days Grace |
| September 16 | "Animal I Have Become" | Three Days Grace |
| September 23 | "Tell Me Baby" | Red Hot Chili Peppers |
| September 30 | "Tell Me Baby" | Red Hot Chili Peppers |
| October 7 | "Tell Me Baby" | Red Hot Chili Peppers |
| October 14 | "Tell Me Baby" | Red Hot Chili Peppers |
| October 21 | "When You Were Young" | The Killers |
| October 28 | "When You Were Young" | The Killers |
| November 4 | "Welcome to the Black Parade" | My Chemical Romance |
| November 11 | "Welcome to the Black Parade" | My Chemical Romance |
| November 18 | "Welcome to the Black Parade" | My Chemical Romance |
| November 25 | "Welcome to the Black Parade" | My Chemical Romance |
| December 2 | "Welcome to the Black Parade" | My Chemical Romance |
| December 9 | "Welcome to the Black Parade" | My Chemical Romance |
| December 16 | "Welcome to the Black Parade" | My Chemical Romance |
| December 23 | "Anna-Molly" | Incubus |
| December 30 | "Anna-Molly" | Incubus |
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