it may take a little more time.  did his previous owner say he was littertrained perfectly?  i think some buns will always leave an occasional poo here and there, i think it’s not a big problem as long as his pee is only in the box.  i’ve noticed that Meadow kicks some poo out of her box sometimes when she jumps in or out… so is it possible he’s not actually going outside the box, it’s just landing there?

It sounds like it could actually still be marking/territorial behavior. The fact that it is just the bottom floor also shows that it may be deliberate. I’d give it a bit more time and continue to put the stray poos into the litterbox. Try to clean up the stray poos frequently, and if you can, spray the floor with vinegar and wipe it down a couple times a day to keep it very clean. Since the house still smells very much like “you” he’s probably trying to get his cage nice and scented like “him”

Sounds like he is marking because he is in a new place and it will subside once he feels secure and safe again. It’s hard for bunnies to change even when the place they are at is wonderful. For prey animals, they feel safe by leaving "messages" the only way they know how, and that is through poops. It sounds like he’s staking his claim and saying, this is my place now. But until he feels secure, he may continue this. SO, actually, if the vinegar and water don’t work or seem to make it worse, you might just leave the stray few around and put excess in the box without wiping up (unless he urinates) so that his scent is still on the floor and he can feel confident that he has his thoroughly left his message.

Once you two bond and he trusts you, he shouldn’t mark as much. So it’ll take some time.

To follow on to what BinkyBunny suggested – are you cleaning his litterbox everyday? If so, try NOT cleaning it every day and leaving some poops in there, it could be correct that he wants more of his scent and not less, so if the cleaning the floor seems to have the opposite effect that you want, consider cleaning his litterbox every 2-3 days as well.

I am going through this as well and I know it is difficult. Especially when you want your bunny to look cute and clean if you have visitors come. Pepper has just been spayed and still drops pellets on my living room floor which was not a good look when my mother in law dropped by for a visit, I’m hoping that cleaning up after her will eventually send her the right message. In her cage she also drops pellets but I tend to leave them as she always goes to her box when she’s there and I figure the rest is territorial. I clean her litter box out every second or third day but in between I sometimes take the most soaked part out and top it up with litter.

I too think he’s marking..MoSimba did that at first esp. everytime he’d get out of his cage. A little poo here and there.
He stopped after a few weeks of being here.

His previous owner told me he would NOT use a litter box, so I didn’t even try for the first few weeks. He just went in one corner
of his cage.

Then I thought I’d give it a shot, since she sent 2 litterboxes with him, and he took right to it immediately. I don’t know what in
the world she was doing wrong, but now he loves his litter box.
Of course everytime I put him on the couch I have to put down a towel, ’cause he’ll pee on it every time. oh well, can’t expect
perfection all the time, lol.

Hey Megan…In the mean time (before he is fixed…) Get a dustbuster!!! This has seriously improved my quality of life hundred fold *laughing* My bunnies mark all around thier litter box in the family room and, Ok, I am don’t mind they are just pills but it drives my boyfriend batty! It’s such a pain to haul the vaccum around for two seconds of use…I asked around and was going to put a “wanted” ad on kijiji.com (free classifieds, there are others too) but a lady from work brought me one from her house! I am sure you can get one cheap new even, but you could try asking around or putting up an add on a free site. Getting a dustbuster for bunny poops is seriously so wondeful!

I need to upgrade to a dustbuster..lol

But for now, since I have hardwood floors, I got one of those swivel dustpans from Home Depot for $12 and keep in the corner. It’s one with the box attached to the long handle that you can sit it on the floor and just sweep everything in. When I first got the bunnies it was killing my back to bend over with a hand dustpan and the vacumm cleaner scared them so bad they would just explode more poops everywhere.

I got a dustbuster for Christmas!!!!  I specifically asked Santa for it, just for the bunnies.  I also have a small handheld vacuum that now I use for the cat litter box areas.  I like the dustbuster b/c I can use it right in the cage & its not as noisy as the handheld vacuum.

Another plus is when you have company over, you just zip the poos up! I do this maybe twice an evening…I always wonder what company thinks when the bunnies throw ‘raisins’ near their litter box in the living room hehe (its much less conspicuous then hauling out the whole bissel and doing that area hehe )

If he’s going in the rest of the house, you should escort him to the litterbox or at least to his cage as soon as you see him marking or lifting his tail to pee. He does need to understand what is HIS place and what is the general territory that he shares, not owns. How much freedom does he have now? You may need to limit it so he can understand his place versus the general area. Xpens are great for allowing exercise while limiting freedom .