Baby bunnies can’t be bonded. All baby bunnies get along with all other baby bunnies, but as their hormones kick in, anywhere from 2 months to 6 months, they will turn into aggressive creatures. They don’t understand familial relationships, so it doesn’t matter to them that the other bunny is their brother. Also, young rabbits are very difficult to sex, so it’s entirely possible that you got a male and a female, who could mate.

You need to keep them totally separate now until they are both neutered. After they’ve been neutered, you’ll need to keep them separate for a month while their hormones drain, then go through the bonding process. You can’t just put two bunnies together. If you go to the ‘BUNNY INFO’ section, there’s a good section on bonding that will explain the process. You can also head over to the bonding forum for advice as you go through the process.

Hopefully, since you separated them before anyone got injured, they’ll bond easily. Please don’t be fooled by them being nice to each other through the fences, they must be kept separate now until a month after they are neutered. There should also be a 6 inch gap between their bars, as bunnies can give each other nasty nips through cage bars.

While they’re separated, it’s a good idea to switch them between cages every other day, so they don’t get territorial, and so the learn the smell of the other bunny. This is known as prebonding.

As a side note, 6 weeks is too young to take a bunny away from its mother.

It doesn’t matter if bunnies are siblings or have been together since they were very young. Once the hormones come into play, everything changes. As has been said, you definitely need to keep your rabbits completely separated now, they shouldn’t be physically together for even a minute. Rabbits dealing with hormones can become aggressive and fight. And they can severely injure each other when they fight. They can also hold grudges when there is aggression and fighting, and never want to be with one another again – even after they are neutered. It does make it more difficult to house them separately, but it is necessary. Depending on your vet, your rabbits may be ready to be neutered now or very soon, so go ahead and schedule their neuters. It will be a while before they can be together again, so it’s best to start them on the road to bonding as soon as you can.