Bunnies really can be litterbox trained very easily!!
Most bunnies self-train for litterboxes, so the steps are as simple as creating a litterbox and putting the bunny in the litterbox. They usually get it. If they don't, they may be telling you something.
Rabbits usually like to relieve themselves in only one or a few places, and they can easily be trained to use a litterbox. Many rabbits get the point if you simply offer them a litterbox where they usually go anyway (starting with in their cage or somewhere in the area they have access to). Also try adding some of their droppings to the litterbox or add some wet newspaper from their cage. Once your bunnies are using the litterbox, you don't need to entice them - but you will need to clean it regularly.
Most bunnies like to munch on hay when they're doing their business, so adding hay to the litterbox will encourage them to go there. Some bunnies like to hang out in their litterbox, so don't be alarmed if you see your bunny napping in there (unless it's very drity, in which case it needs to be cleaned). The litterbox is a safe place for the bunny.
Some bunnies like to have their litterbox cleaned after each use, while other bunnies think that if you clean it every time, you are telling them that it isn't where you want them going. You'll have to pay attention and figure out where your bunny stands on this issue. He understands the litterbox, he just doesn't understand you yet.
You will probably always find poops outside the litterbox. This is normal, and not an indication that your bunny isn't using the litterbox. Rabbits use droppings as territorial markers, and in the wild they also lead the way back to safety via a zig-zag path (never straight to the entrance to the warren). Also, it seems that almost everything sticks to their little poops, so one day you might find one in your pocket. Sometimes when a bunny hops out of the litterbox, one or two will follow him out.
If the litterbox has an ammonia smell, it should be cleaned immediately!!
Another way that you'll know if the litterbox should be cleaned (or moved) is simply that you'll discover that one of your bunnies has turned it over and made a fine mess of the contents. Sometimes this means you're not doing your job well enough, and sometimes it means your bunny is mad at you. Of course, sometimes it just means your bunny is having fun at your expense.
Some bunnies have the best intentions, but will back up to a corner of the litterbox and wind up peeing over the edge. If you have a bunny like this, please get a litterbox which is higher on 3 sides or even enclosed on 3 sides to prevent mess.
NOTE: Do NOT use cedar or pine shavings with your small mammals!! (Aspen wood shavings are exempt from this warning as they are safe for small mammals - it's a hard wood and specially prepared for bedding or litter for small mammals, including washing and kiln-drying).
Please see these articles on wood shavings (especially aromatic woods like pine and cedar) and the problems they introduce for small mammals. An excerpt reads:
which are known to cause liver disease (quoted from the U.S. Dept. of Health and Human Services guide for the care of laboratory animals). Use grass hay (on top of newspaper) or organic kitty litter for your rabbit's litter box and timothy hay for other small animals' cages.
The above quote can also be used to get yourself out of conversations, as most people will have no clue what you just said, nor will they be inclined or able to dispute it.
To clean and disinfect, ideally you would a product called Vanodine, which is totally safe for animals, even if they ingest a small amount. It is a non-toxic and very thorough disinfectant - it kills virii, bacteria, and even fungi. It is a good replacement for chlorine bleach, which also kills everything but is much more dangerous to animals. After using bleach, you must be careful to thoroughly dry the litterbox (preferably in direct sunlight) everything so there's no trace of chlorine left. Some plastics will also absorb the smell of bleach. Vinegar is a good cleaner but it is not a disinfectant. You can also try vanilla extract - it is a good cleaner and disinfectant too!! (Part of the reason for that is the 20% alcohol content, which evaporates quickly).
If your bunny seems to have forgotten its litterbox habits... Bunnies don't forget their litterbox training. When they start going outside the box, it is usually because they are complaining about something, and this should be investigated. It is possible that a UTI (urinary tract infection) or bladder sludge or stones is making it uncomfortable for the bunny to urinate, so the bunny will "forget" the litterbox as a way of calling attention to the problem, and asking you to investigate the leavings. This is actually very important, and an early warning that something is wrong. If your bunny starts behaving like this, please try to determine the underlying problem and make an appointment with your vet.
If you notice chalky calcium deposits in the litterbox... Rabbit urine is typically mineral-rich, so the presence of calcium in the urine should not be interpreted as the only indicator of bladder sludge or stones, but thatis not to say that it isn't a concern. Rabbits, like all mammals, need calcium in their diets and some of it will be eliminated in the urine, and rabbits' urine is rich in minerals from their diet. Seeing calcium or chalky buildup in the litterbox doesn't necessarily mean there is any build-up of calcium in the urinary tract. You should observe your bunny when he/she is in the litterbox, and watch for signs of straining, struggling or discomfort. Also check what's left behind (if you can) to see if it looks normal. If the rabbit is showing any signs of calcium buildup in any form, then it's time to talk to the vet, and perhaps get an x-ray of the bladder (calcium shows up very nicely in x-rays).
If you notice odd coloring in the urine... A rabbit's urine can be anything from clear to thick yellow to brown to even bright red and still be considered normal (unless the bright red is blood, but it often isn't). Something as simply as a change in the diet or stress can cause a rabbit's urine to change color and/or clarity. Only in certain cases is bright red urine actually blood (and you'll be able to tell by smell), which indicates a serious problem and the bunny should see a vet right away.
If you notice small poops... Small poops usually indicate the beginning of a blockage, and the size of the poops indicate the largest size of anything that can pass through the bunny's digestive system. If the bunny is shedding, you will likely see the poops strung together with the swallowed fur.
If you find small clusters of pungent soft poops... Rabbits have two different kinds of droppings - fecal, the typical round and basically dry and odorless droppings, and cecal - or cecotropes - which are meant to be re-ingested by the rabbits. In much the same way a cow will regurgutate its cud to chew it, rabbits re-ingest their cecal droppings, sometimes directly from their anuses, to gain all the nutrients from their diet. This is not only normal, but essential to the rabbit's health - you should worry if your rabbit doesn't eat its cecals. These used to be known as "night feces" (they are not feces, they come from the cecum, not the bowels) because rabbits would usually eat them at night, but it's theorized that this is because it was stored up food from a dusk of forraging for foods and not fully digesting them before returning to their warrens. Please read Dana Krempel's article The Mystery of Poop to learn about cecotropes.
If your bunny has runny stool and/or poopy butt... The first thing you should do is clean the area, very gently. You can use plain cornstarch (NOT TALC) to give a dry bath and hopefully remove most of the mess, and if necessary, have your bunny sitting in a very small amount of warm water to soak the toughest clumps. If the bunny must get wet, do your best with towels and a hair dryer set on a low setting to dry the fur - wet bunnies can get sick easily. The next thing you should do is change the bunny's diet, eliminating sugars (all fruit), limiting greens, and promoting fresh hay to eat. You should also contact your vet and tell them of the situation and see about making an appointment. Check the bunny several times a day and clean as necessary. Look for an improvement very soon (in a couple days) or make an appointment to see the vet. Poopybutt can easily lead to flystrike or infection. (another article on flystrike). Please read Dana Krempel's article The Mystery of Poop for a better understanding.
If you notice your bunny isn't pooping at all... If your bunny hasn't pooped for over 12 hours, call your vet immediately, as this may indicate a blockage in his digestive system or stasis or something else equally life threatening. If the bunny's digestive system shuts down, it can very easily die in a day or two - if something like this happens on a weekend, you will need to go to an emergency vet. Don't know of an emergency vet near you?
What to put in the litterbox? You should avoid using cat litter, as some of it may be toxic to rabbits, and they may eat the litter. Some of the following ideas may help:
This is Cocoa and Brownie in separate litterboxes, one used as a litterbox and the other used as a haybox (it will eventually be used for litter, and then I'll clean the other one and the functions will reverse).
Brownie disappears into a giant bag of hay (and I finally understand why it occasionally seemed haunted). Note that the bag had many holes and rips in it so that it could breathe and no moisture would collect, which would cause mold to grow.
Tamari and Noffy sharing the litterbox inside their cage (or "home within a home" since it was only ever used as a cage during bonding so they didn't hurt each other). This one was a simple cardboard box lined with newspaper and hay, but they liked it just fine, and they had a few other litterboxes around the house, for when they were causing trouble.
San Diego HRS page on setting up a litterbox
Medirabbit's article on bladder sludge, sand, and stones (pdf)
Medirabbit's article on the differences between normal urine and sludge
The House Rabbit Society's explanation of cecotropes
Article about dealing with territorial marking and urine spraying
The House Rabbit Society's FAQ on litterbox training rabbits
The House Rabbit Network's article on litterbox training
The MA House Rabbit Society's article on litterbox training
This shows how to set up a litterbox with a lighting grid
Some solutions for litterboxes for your rabbits.
Long Island Rabbit Rescue Group's page on litterbox training