Watched it when I was a kid, a long time ago... I can only remember that a girl (princess or daughter of someone important) has been injected with some kind of virus, and then you follow the action inside of her, where bacterias are soldiers and stuff like that. I think it was Japanese but am not sure.
Guest, I think the best match in Crow T Robot's link above would be the Korean pseudo-anime film Space Transformers (AKA Micro-Commando Diatron-5) from 1985, where Ivy, a special girl who protects the universe, is infected with bacteria and a special team is shrunk down and injected into her to battle it. The entire movie is currently available on Youtube here.