Doesn't need to be in pixels.
(but a printer would expect to see 300dpi, if you were gonna send artwork.)
remember that 12cm x 12 cm is just the very front, and you need to worry about "bleed" areas outside that; then there's folds to worry about too: if it's an album jewel case this'll be slightly different to single jewel cases since the spine is thinner on single cases. Also album cases have a seperate back insert; single cases don't.
have a look here for an example of the single version:
http://www.wizbit.net/downloads/cd_a..._flattened.png
the album kind is slightly more complex, i suggest you take one apart and look at it. the front will be essentially 12cm square but the back has a roughly 6mm tab on either end to make the two printed spines (often but not always the same), and is wider than it is tall, but they *do* vary slightly in how they work.