I’m don’t know if mice can harm rabbits in any way (transmitting diseases, etc).  But the best thing to do would be to set up some traps around the pen area or in your kitchen.  There are humane traps you can get.  I found this one amazon:

http://www.amazon.com/Smart-Mouse-Trap-Hum…B000YFA7HW

ALSO, could the litterbox full of hay and open cage attract mice? If so, what should I do? o-o

Hay definately attracts them. It’s what brought mice into my place. Pretty certain that’s how Jersey and Rumball got fur mites too. My vet said fur mite most commonly brought via mice and birds. You want to keep watch for that. Even talk to your vet about giving Binksy a preventative dose of Revolution. Mice don’t really hang out in a place that’s going to be disturbed alot like a litter box though. It’s more where you store hay. I had mine in a big box near the house and that attracted them. The then made their way inside.

Someone on here said mice or rats can be attracted to the rabbit dropping also.

When I had mice I caught them in a humane trap. Once I had them out of the house I checked over areas I thought they could get in and blocked them off with steel wool. I also used peppermint oil on a cotton ball as a deterrant. I only had 2-3 mice (or possibly same one came back in) so it wasn’t too hard to deal with them.

We had a major mouse problem at my house a year or so ago. I have birds too, so there was always seed and stuff on the ground, even if I vacuumed a couple times a day (which obviously isn’t always possible since I am not always home!).

For me, things got serious when I found mouse poo in my bird’s cages. EWW! Not to mention they can be dangerous, especially to a tiny bird! I ended up putting Riley (the rabbit) in a small cage that I could place up off the ground so that the mice couldn’t get to it, and then placing traps all over the house. Sadly we had crazy smart mice (we watched them physically jump over the traps to avoid them, despite yummy peanut butter and cheese!), so we eventually had to resort to poison, in order to keep my babies safe. I hated doing it (I don’t even like snap traps), but my feathered and furry baby’s health had to come first!

After we had the problem under control, my Mom looked into getting an exterminator out to the house to go around the outside of the house and find the little cracks and holes the mice can get into to hopefully prevent them getting in in the future. They can get in tiny holes you can’t even see. We haven’t had a problem since, but I also moved out with the animals, which I think were a major attractant to the mice.