It is a seed right? If its not paleo would there be counter-recommendations for someone trying to improve their immune system?

It's one of those tiny details I think most of us don't bother fussing over it.

You're asking about common black table pepper, right? And not "peppers" like chile peppers?

If so, black pepper is not the seed. It is the dried immature fruit of the Piper nigrum plant, a perennial vine common to South India.

Fruits are permitted in Paleo, right? Therefore I should think pepper is, as well.

Yes I was asking about black table pepper. Not nightshades.

I doubt that black pepper is really "paleo". I do not have to worry about it because I am allergic to black pepper. (& white pepper) I do not keep it in the house & avoid it when eating out.