If you're having girl problems I feel bad for you, son
I've got 99 problems but a bitch ain't one

from Jay Z – 99 Problems Lyrics on Rap Genius

Meaning

This hook is, um, “borrowed” from an Ice-T song also called 99 Problems

As Jay-Z notes in his 2010 released autobiography, Decoded, This line refers to an incident in 1994 where he was pulled over, refused to let the cops search his car, and police dogs (literally, ‘bitches’) were called in to sniff his car for drugs but never showed up, which fits, considering that the song is about racial profiling. So he’s got hella problems, but a bitch isn’t one of them.
The line is clever on another level, though, when considering that he is paralleling the problems dudes have with women to not having a problem with a literal bitch (a police dog).

The hook itself has been profiled repeatedly over the years as an example of misogyny in hip-hop. You can see Jay decoding the song, discussing that perception, here:

http://www.youtube.com/watch?v=fSP7cY2uzPY

See also this interview from NPR’s Fresh Air. The discussion of “99 Problems” begins at 35:33.

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