I am having this issue with my adopted rabbit as well and he is supposed to be litter trained. He always pee in the litter box except for the first few days when he was just adopted. The pills are all over the place though most of it is still in the litter box.

This is from the House Rabbit Society litter training page.

http://www.rabbit.org/faq/sections/litter.html

8.9 Pills vs. Urine.

All rabbits will drop pills around their cages to mark it as their own. This is not failure to be litter-trained. It is very important for your rabbit to identify the cage as her property so that when she leaves the cage for the bigger world of your house, she will distinguish the family’s area from her own and avoid marking it. To encourage this, make the rabbit the king of his cage. Try not to force him in or out of it– coax him. Do not do things to his cage that he doesn’t like, or things to him that he doesn’t like while he’s in the cage.
The trick to getting the rabbit to keep his pills in the cage is to give him ownership of his cage–respect the cage as HIS:

Don’t reach into the cage to take him out; open the door and let him come out if and when HE wants to come;
Don’t catch him and put him back in the cage or it will be his prison, not his home. Herd him back gently, and let him choose to go in to get away from you (I walk behind my buns, clap my hands, and say “bedtime.” They know that I’ll not stop harassing them with this until they go into their cage, so they run in except when they feel they haven’t gotten their fair share of time outside the cage.
It’s a bit like a child going home and closing the door, because someone is calling her names. They may make the playground an unpleasant place for her, but they can’t bother her in her own home.
If the rabbit has been snuggling with you, it’s okay to carry him to the door of the cage and let him go in–just don’t put him directly into the cage, and never chase and trap him and put him in the cage.
Don’t reach into the cage to get food dishes–anchor them near the door of the cage so they can be filled with a minimum of trespassing into the cage, or wait until the rabbit is out to fill them.
Don’t clean the cage while the rabbit is in it–wait until he comes out. He’ll come over and supervise you, even help you move things around that you’ve set down outside the cage, but as long as he isn’t in the cage, he won’t see your cleaning as an invasion of his territory. (Smart rabbits–I wouldn’t object if someone were cleaning my house, either… 🙂 )
The same technique can be used if a rabbit doesn’t live in a cage, but in a particular part of a room. Mark the territory with a rug, tape, whatever, and don’t trespass over that.

You aren’t putting litter all over the bottom of his cage are you? Just in the litter box, right?

You might find he gets better after he is moved in the house. Sometimes they don’t do as well if they don’t like their set up, so if he’s happier in the house with you, he may use his litter box more completely. Also, make sure the box is gig enough for him to sit in it comfortably. If he is pooing in one spot in the cage more than another, try moving his litter box to that spot. Also, try scooping up the poos and putting them into the litter pan repeatedly, so he gets the idea that wherever he left them, he’s going to find them in the litter pan. He may lern to associate it as the place to do all his business, not just pee.

I assume at 4 months he is not been fixed. Many times after they are fixed they almost just start using the poop dish as second nature. My 3 buns are became much better after getting fixed (male and females).

I got my buns spayed/neutered between 4-6 months also. I’m not sure whether it’s related to forming a bun’s personality but that’s when they reach maturity. Spaying definitely helped to improve on litter training. After a few years, my buns still leave their poop here and there. I’m very jealous of those with buns that use their litterboxes religiously.

I think that you definitely should neuter your bun as soon as he is old enough – it definitely helps prevent any behavioral issues and aggression.

How often do you pick up the poops? I know it is kind of a pain, but the way that my husband and I always litter train our bunnies is by keeping their living area pretty much spotless and dumping any poops into the litterbox. This means that for awhile we will shop-vac their cage twice a day, and use vinegar on the floor to clean up any pee until they learn that the cage floor needs to stay clean.

What is the litterbox like? Make sure you have a nice big square one, not one of those teeny little corner ones. You can buy very inexpensive ones from Target or Walmart, they are cat litterboxes. I also have used short rubbermaid bins as litterboxes. The bigger the better! I also put a layer of hay on top of the litter. Hay should be in the box, or in a rack hanging over the box because bunnies will poop during or right after they are done eating.

You have received some great suggestions. It is definitely challenging with young and/or unneutered bunnies. Territorial markings, where they are spread all over the place instead of only piled in the corner, should lessen when the hormones die down about a month after spaying/neutering. Is there any reason your bunny is in the garage and not in the house? Do cars actually drive in and out of the garage? Do you have any other animals, like dogs or cats that come around your bunny’s cage?

Once he is neutered and living indoors, he should become better with his litter habits. I would not wait to bring him inside. I can’t imagine that a garage gets very good air circulation and light if it’s closed, and it’s not secure if it is left open. You might not put him into the NIC condo right away, but you can still bring his existing cage in and get him used to the house. Some buns need to reclaim any new living space, so even if he is perfectly trained in the garage, be aware that you might need to start over again once he’s inside. As long as he is peeing in the box exclusively and getting a lot of the poops in there, I would consider him littertrained at this point. “Perfect pee” is sometimes the best some bunnies will do, especially being unneutered.

Sounds like my Komoko is indeed litter trained. I switch to a new litterbox so he got more space in the cage and he peed and pilled only in one corner of the new litterbox with a few pills around the cage.