Well, there are "little people." The African pygmies quite clearly exist (Although they are facing discrimination and have been victims of genocide, sometimes because people believe that eating their flesh gives you magical powers and sometimes just because the other locals don't like them.) and then there is of course Homo Floresiensis which are believed to have been alive as little as 12000 years ago.
...But those two groups seem unlikely to have been the cause of the stories in places far as Europe and America. Personally I think that the cause for the stories of little people being so popular is either due to dwarfism or simply the fact that "they look like us but smaller" (or bigger in case of the giants) seems like an easy thing to invent if you are thinking of magical creatures.
