I recently started playing keyboard and have noticed that sometimes after playing a challenging piece or playing for a long time my hands ache. Not badly, but enough to make me concerned that I'm not playing quite right. Since I don't want my hands to get messed up, I was wondering if anybody maybe had an idea as to what I could be doing wrong?

I'm not aprofessional pianist or anything but I have three theories as to what happened.
1.You just played a lot and aren't used to it.
2.You are holding you elbows to high
3.You are stressing your fingers/they aren't strong and you need to excericise them

If the problem is in the joints of your fingers then you might have a problem. Just hope you don't have carpoltunnal (sp?).

If it is the wrist area that aches then you are either holding them too high or too low. (Most begginners will be too low because they get lazy.) This puts enormous pressure on the area if you are playing a difficult passage.

If it is the forearm area then that just means that your arm stamina isn't up to the level yet and all it takes is more practice to raise it. I've been playing for 10years and my forearm still get the "burning" feeling like I just worked out for 2 hours in the gym or something if I play a fast paced song for too long.

If your hand simply becomes unstable (shaky) then it just means its tired so give it a rest before you play more. You will notice a minimal amount of aching on the back of your hand but no pain. Your hand feels weak and that's about it.

After reading you responses I think the problem is in the way I hold my wrists and my stamina. Sometimes my right hand thumb joint hurts a little bit, but I think that might be the pain in my wrist running up my hand, as most of the pain is in my wrists and forearms. Thank you both for your help:)

Umm...You're welcome.