Is it
¿Qué clases estas tomando?
or is it
¿Cuáles clases estas tomando?
Both are ok
Same as in English you can say:
What classes are you taking?
or
Which classes are you taking?
Don't forget to use cuáles and qué with acute accent when those words are used in questions and also remember to add the ¿ opening question mark.
I don't agree with DGaleano, his sentences are not incorrect but they would sound a bit odd, at least in Spain. The verb "tomar" is not frequent in this context in Spain.
My university years are long past but I think that if you want to know which courses (being class a slightly more informal term for 'course') are been taken by a fellow student this semester, you can ask
¿A qué clases vas a apuntarte?
or
¿En qué clases te vas a matricular?
or
¿Qué clases vas a coger?
You can replace "clases" by "asignaturas". I used the second term when I was a student but they are interchangeable. The last sentence is closer to yours, in translation terms (coger = take). You can also use "cuáles" instead of "qué" but I prefer the last one.
Notice that the verb coger may sound rude or out of context in some Spanish speaking countries like Argentina, meaning "making sex". I'm not sure if they use it in this context as just an equivalent of "take", but be aware. The other two options are perfectly fine in all places.
The verb tense used depends on the time when you're asking in relation with the inscription in the classes.
Before the inscription (future):
During the inscription, when you're signing the forms:
After the inscription:
As pointed by wimi you can use the future any time at the beginning of the scholar year. If the inscription has been made or not, it's not relevant: