During lyssavirus surveillance, 350 brains from four species of fruit bats and one species of insectivorous bat were collected from seven locations in Northern Nigeria during May to October, 2006. Lyssavirus antigen was not detected in the brains, and isolation attempts in mice were unsuccessful. However, serologic tests demonstrated the presence of lyssavirus-neutralizing antibodies in bat sera. Of 140 sera tested, 27 (19%) neutralized Lagos bat virus, and two of these additionally neutralized Mokola virus. The positive samples originated from the straw-colored fruit bat (Eidolon helvum) and the Gambian epaulet bat (Epomophorus gambianus). No neutralizing activity was detected against other lyssaviruses including rabies, Duvenhage, and West Caucasian bat viruses.