Keep two or more litterboxes outside the cage and one inside the cage. As his habits improve, you can decrease a litterbox or two. If you have more than one rabbit, you may see less control and more marking. If slip-ups begin, start shorter periods of freedom and more litterboxes. Keep litterboxes very clean.
Rabbits are very clean creatures.
A smelly, soiled litterbox could cause your rabbit to choose another place to do his business, sometimes just outside the box. Depending on the number of rabbits and litterboxes, clean litterboxes at least once a day. Spritz litter pans with white vinegar to clean and deodorize. Let pans soak if there is urine build-up and then rinse clean. Do not use chemicals.