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They do this when they're stressed. It's a reaction to their fear that something else might eat them (although not very logical, I agree!). It also tidies up the nest if the babies die of natural causes.
We had a very young gerbil who did this, and I think she was just a bad mum and got stressed out by having the babies around. It's upsetting, isn't it? We kept wondering if it was our fault, if we had stressed the gerbil out by looking at her etc. They certainly like to be left alone when they have babies, I know.
So, the rabbit mum was stressed. It might have been something to do with her character, or it might be something you could change if she has babies again. Good luck and don't feel guilty - small furry animals die a lot, unfortunately.
This happens often and, as flossheal says, its usually due to the mother feeling stressed or unsafe. Make sure that the mom has a place where she can hide her nest, like under an overhang where she can feel hidden from predators (remember that she is a product of evolution. She doesn't know she is safe. Her instincts say she is in the open.) Leave the nest alone after the birth.
Along with climate change, scientists are observing what is called "Diet Change" among many species of animals. Up until the last 15 years, rabbits and many other species of animals have not been observed to eat their young. So don't worry if you look at somebody's kid - maybe your own - and suddenly develop an appetite. Yes, your rabbit will have more kits - when she is hungery.



Why did my rabbit eat her kits?
Well, my rabbit is three years old, and I had just gotten her about 2 to 3 months ago, well the day before yesterday, I noticed she was nesting, so I left her alone and about 1 or 2 hours later I looked in her cage and found her eating one of the kits....
She only had 2 and they were both dead, not even in the nest, It was her first litter. When I went to remove the kits yesterday, I found her trying to cover up one of the kits, who's body was half eaten. I just wanted to know what could have happened to cause her to do this, and can she have another litter.