The litter box should be inside the rabbit's cage. The rabbit should have access to the litter box at all times, otherwise he (or she) will never properly litter train and will soil his cage.
You might want to put additional litter boxes outside the cage, for when he's allowed out. This is an especially good idea if your rabbit's allowed out in more than one room, or if you're in the process of litter training. However, always leave the main litter box inside the cage, in case your rabbit wants to run back there and use it.
Many rabbit cages sold in stores are too small. The cage should fit the litter box and all other necessary supplies, and still leave enough room for your bunny to move around and stretch out.
Make sure you use a safe litter material in the rabbit's box. Cat litter (clay litter) is dangerous for rabbits. Corn and wheat-based litters are not recommended, either, because if your bunny eats any of it (which is likely), it's unhealthy and can lead to illness. Safe litters include:
Put some hay in your rabbit's litter box. This will encourage good litter habits, because rabbits like to nibble as they use the washroom.
See the related questions below for more info about rabbit care.
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