In the song, Jay-Z tells a story about dealing with rap critics, racial profiling from a police officer who wants to search his car, and an aggressor.

In creating the track, Rubin used some classic 1980s sample staples such as "The Big Beat" by Billy Squier, "Long Red" by Mountain, and "Get Me Back On Time" by Wilson Pickett.

The title and hook are derived from Ice-T's song of the same name from his 1993 album Home Invasion, which featured Brother Marquis of the Miami-based 2 Live Crew.

Ice-T would re-record his version of the song with the Rubin/Jay-Z guitar riff for Body Count's 2014 album Manslaughter in order to "reclaim" the hook from being mis-attributed to Jay-Z.

[4] Portions of Ice-T's original lyrics were similarly quoted in a song by fellow rapper Trick Daddy on a track also titled "99 Problems" from his 2001 album Thugs Are Us.

In a discussion at the Celeste Bartos Forum at the New York Public Library,[5] Jay-Z described the second verse of the song as representing "a contest of wills" between the car's driver who is "all the way in the wrong" for carrying illegal drugs, and a racist police officer who pulls over the driver not for any infraction but for being African American.

"Both guys are used to getting their way" and thus reluctant to back down, Jay-Z notes, and the driver "knows a bit about the law because he's used to breaking it" and asserts his legal rights.

14 on Pitchfork Media's top 500 songs of the 2000s (decade) and in October 2011, NME placed it at number 24 on its list "150 Best Tracks of the Past 15 Years".

On January 21, 2009, Jay-Z performed the single as part of his set at the Staff Ball, the last official event of Barack Obama's inauguration.

Jay-Z tweaked the lyrics to suit the historic atmosphere, and the crowd sang along: "I got 99 problems but a Bush ain't one", replacing "bitch" with the name of the former President.

"[17] Eminem referenced the lyrics in his track "So Much Better" on The Marshall Mathers LP 2 album, with the lines "I got 99 problems and a bitch ain't one/ She's all 99 of 'em; I need a machine gun".

[19] In 2009, fellow rapper and collaborator Kid Cudi, referenced the hook in the opening verse of his song "Soundtrack 2 My Life" with the line "I got 99 problems and they all bitches".

The singer Hugo recorded a bluegrass cover in 2011 and featured in "Girlfriends", the fourth episode of the TV series Reboot.

It consists mainly of scenes filmed in close proximity to Jay-Z's childhood home, The Marcy Houses in Bedford Stuyvesant.