"Taming" a shy rabbit

Recently I adopted Rupert, a young Giant Chinchilla. He's almost 12 weeks old now. He's been with me for 3 weeks. I was looking for a friendly house rabbit and was told the Giant Chin is a very affectionate breed.

Rupert is afraid of me and very skittish. He isn't neutered yet. I keep him in my hallway between my foyer and the bathroom, between two baby gates. I pass through the hallway during the day. I usually talk to him while I'm there and I reach down and offer my hand for him to sniff often. He will sniff my hands or my feet, but will not allow me to touch him in any way. If I make a noise he darts away. If I do something like tossing some hay into his litter box, he runs away. He won't accept treats or vegetables from my hand, as my other rabbits do. I have to put them on the floor nearby.

He seems to accept the cats when they enter his pen, he will approach and sniff them and allows them to sit near him. He has a couple of boxes where he can hide. So, how can I tame Rupert and help him get over his fear of me? Should I remove the hide boxes? Would neutering him help to make him less skittish?

Do NOT remove the hide boxes, he'll most likely freak out that he can't get to a safe spot.
Try having a treat/veggies NEAR you, then maybe in time he'll eat out of your hand.
Whenever your reading a book, on a device etc. Its best to just sit in the area and let him come to you (try not to touch him the entire time he's sniffing you) you just have to be really patient, he'll let you know if he wants to be petted (lowers his head/pushes his head under your hand) if you do need to bring him to a different place (vet, etc.) I suggest putting a treat in a carrier and carry him in the carrier , so you don't scare him by holding him.
Neutering may help, but I think he just needs to get used to you.

Spending time sitting with him in his pen(or other small area) is usually what will help him bond with you the most. It doesn't necessarily have to be in his pen, but you do want to be in a smaller area so he can't just run and hide the whole time. Whether or not you remove the hide boxes depends a lot on how he responds. It's better that when you are sitting with him, that he doesn't just run and hide the whole time, but you also have to make a judgment if removing the hide boxes makes him too stressed that it's actually setting the bonding process back.

Every rabbit is different, so no one way is the right way. I will usually just start trying different things and judge how each rabbit responds, because they all respond differently. I'll try removing the hide boxes because for some rabbits it can be counter productive and heighten their nervousness if they are able to just run and hide from you the whole time, for some rabbits I'll keep the hide boxes as it makes them too stressed to not be able to hide, I'll try using their usual treats to help encourage them to be brave, for some rabbits it works to spend time holding them as it helps them realize they actually are safe, some rabbits it's better to not hold or pick up at all as it freaks them out too much. But in everything I try, I always pay close attention to their body language. Some nervousness is to be expected and is ok if it's not excessive, but if it's excessive or they are freaked out at all, then I will back off and try a different method. It's just trial and error to figure out what method is going to work best for your own bun.

I had one rabbit that was so nervous when he came to me, that he freaked out and ran to the other end of his pen every time I had to reach in to clean. He was so nervous being in a new home and around people, that it upset his gut and eventually he went into stasis, a very serous case of it. Two things that worked to help him come round and feel safer. One was that I had a girl bun that he seemed interested in and she seemed interested in him, so I put them in pens side by side. He was so much happier and calmer after that. So having a friend next door can help a lot in helping them to settle in better. Though you do have to make sure that both rabbits are happy being next to each other(usually not two unneutered males), as if they don't like each other then it can actually make the shy rabbit more stressed. You could even use your cats in a way. If he seems comfortable with a certain cat around, have that cat there with you when you spend time with him.

The other thing that helped my rabbit to learn to trust me was because he was sick with stasis, I had to syringe feed him every few hours and give him medicine. And it was actually that contact with me that helped him learn to trust me. Maybe it was also because he got some tasty medicine which he really liked the taste of. After those weeks of nursing him he was very affectionate towards me and loved being around me. Now that wouldn't work for every rabbit as some rabbits detest being held, syringe fed, or given any medicine, but for him it worked perfectly.

Sometimes it just takes time. Some rabbits can be extremely nervy and it just takes a lot of patience and time to gain their trust. But it's all a matter of exposure. The more time they spend around you, the better chance they have to learn they are safe and can trust you.

You might want to take a look at this link as it has some good tips on bonding with rabbits. The other link is understanding how rabbits communicate if you haven't already seen it.
http://flashsplace.webs.com/bondingwithyourbunny.htm
http://language.rabbitspeak.com/

One thing I wonder about is whether it's a good idea for Rupert to be kept in a "high traffic" area. The cats and I go in and out of his pen all the time, and even when we're not there, it's near the kitchen which can be busy and noisy. When I put him there, the idea was to expose him to traffic and noise so he'd get used to it and lose his shyness. Not only is his shyness not improving, but three weeks later he seems to be getting worse. He used to nuzzle or nibble at me when sniffing, now it's a quick sniff and he takes off.

Right now I have Saoirse in a pen in my closed bedroom where there isn't much traffic. This is temporary until I can get her spayed. She's very friendly, and I feel badly that she's in a quiet place on her own, even though I do visit her several times per day. She's also growing rapidly and is starting to outgrow the pen. I'm wondering if Rupert might do better in a quiet area where he feels safer, or if being more alone could make him even more shy? If I moved him, I'd still visit him throughout the day.

If you feel that the new area has made him get worse, then yes, I would move him to a quieter area if possible. But still try and spend as much time sitting with him as possible, as it will be this quiet time with you that eventually brings him around.

The other thing that you may want to consider trying, is seeing if he and your girl bun have any interest in each other. You want to have a pen between them just in case they don't respond well. But it is something that I would consider doing myself when trying to help a nervous bun settle in better. If they respond well and it's possible for you to do, I would put them in side by side pens. Since she isn't spayed yet, then you do need a mesh barrier small enough that they couldn't breed through the bars(yes, it can happen). I use 1/2 inch hardware cloth, and that can be zip tied to the bars of your pen. It might mean they each have a smaller area temporarily, but personally I feel it's better to have happy rabbits temporarily in a smaller area, then unhappy rabbits in a large area.

Things to be aware of if you try this. The rabbits can respond badly to each other and even though they won't be able to attack each other with the pen bars between them, it could make your male bun more nervous for a little while after they have been separated and back in their own areas. Though I will say that this isn't common when it's a buck and doe. Male/female is usually the best combination for getting along. The area you introduce them in may make a difference how they respond to each other too. If you bring the doe next to the males area, that is usually better since does can sometimes be territorial, or a neutral area, but it may not make a difference for your buns. The other thing would be that if you do put them side by side, this could result in the start of hormonal spraying(which is a pain).

eta: If you do put them in pens next to each other, you also need to make absolutely sure neither can jump the barrier so you don't end up with a pregnant bun.

My rabbit was the same way when I got her, she is a lot more friendly now but still has a ways to go. I would sit in the pen with her every day and just ignore her. I would do work in there, go on the computer, read, and even take a nap in there. She eventually came out and sniff me and learned that I was not scary because I did not touch her. It was time consuming but sometimes they take a while to trust you.

Time and patience are the keys. Most rabbits take time to gain their "trust". The more quiet time you two have, the better. Also, I hand feed herbs like Cilantro and have on that was the shyest bunny ever will come when I call her and will walk on her back legs for Cilantro--the second mini rex to do so.

Lots of good ideas and excellent suggestions, thanks everyone!

I've had to do a lot of thinking and logistical planning. I've decided to move Rupert to the bedroom, which is quiet and will have a lot fewer interruptions. If anything he's getting more skittish rather than less. Tonight I walked past the gate with a plastic bag, when it crackled he panicked and took off down the hall. Later I tried to give him a piece of banana, as usual he won't touch treats unless I leave them on the floor and go away. When I try to spend time with him in the hallway, my little feline attention sponge inserts herself in between me and Rupert. She's sweet, but she doesn't like to share. She does this when I pet any animal. Also, the hallway is a big area and Rupert isn't that big yet. Saoirse on the other hand is growing like a typical Flemish Giant and has pretty much outgrown the pen in the bedroom.

Right now I use steel gates to block off the ends of the hallway. Saoirse is big enough now that she could easily jump over the gates. So I had to spend some time figuring out how to prevent her from jumping while still being able to easily move any barrier I install above the gate. Luckily I have an old plastic baby gate that has hinged attachments that can be bolted to the wall so that the gate can swing out of the way. I'll just remove the steel gate at the other end. The two steel gates can't be stacked because they have a steel bar along the bottom.

So tomorrow I will do the move. I don't think I'll be able to pick either of the rabbits up. With Saoirse my main concern is her size, she's a lot bigger than the last time I picked her up. I've already put my big plastic dog crate in the hallway with Rupert after removing his hide box. That way hopefully he will go into it on his own or at least get used to it. If not - I'll see if I can lure him in with food or treats. He will get his hide box back after the move.

Once he's in the crate I will clean out the hallway area, there's some poop on the floor and the litter box needs to be changed. I'm not sure whether to leave each area smelling of its current resident or to use vinegar to get rid of any scents. Either way, I'll change the box and clean up the poop. Next I will open the bedroom door, then use the pen to "herd" Saoirse into the hallway pen. Once that's done, I'll clean the bedroom area and Rupert can go into the bedroom pen. I'll switch the litter boxes as well, since Saoirse needs a bigger one now!