I have to agree my cats have always gone in there litter box even when sick with the runs. so you may have to make a trip to the vet. Is she uptodate on shot and dewormed? If not that may be the problem (worms)There are lots of diff kinds. But yes keep her confined to a small room till she starts using the box and make sure she has a clean box.(have him) Scoop it atleast 1x a day some cats dont like to have a dirtybox and will not use it if it is. I hope she gets better and keep me updated. good luck