"What do mice eat?"
Translation:Co žerou myši?
CO means WHAT, so you ask that when it's very general - like here.
JAKÝ means WHICH/WHAT and is used when it's less general and should be followed by a noun, e.g.: "Jaké maso jíš?" - "What (kind of) meat do you eat"?
Finally, you have KTERÝ, which can basically only be used as WHICH and you have to provide a selection (or it has to be implied). For example: "Který tým máš nejraději?" - "Which team do you like the most?"