I am not sure I would say that there are many differences between boy and girl kittens, but for the sake of our conversation, let me try to describe them.
The first thing you will notice is the gender difference in their eyes! Female kittens have large round “pupil-less” eyes while males have very defined blue irises. This difference is so prominent that even your vet can tell by looking at their eyes alone whether they are male or female cats!
You might also notice when one kitten looks up toward you it may appear as though he has his ears back compared to another cat in the room. Male cats tend to grow much longer fur on top of their head than females do. Another obvious difference is that male cats develop deeper voices over time whereas female voices stay relatively constant throughout life.