Vlgr1 (very large G-protein coupled receptor 1) knockout mice against hybrid backgrounds of the 129/Ola and C57BL/6 mouse strains show hearing deficit and high susceptibility to audiogenic seizures. The present study examined how hearing impairment and susceptibility to audiogenic seizures in Vlgr1-deficient mice change according to the genetic background of 129 and C57BL/6 mouse strains, which are popular strains for genetic studies. C57BL/6 mice have normal hearing ability during adolescence and are resistant to audiogenic seizures, and the 129S1/SvImJ substrain does not have a severe hearing deficit or convulsions as a result of audiogenic seizures; therefore, these strains were chosen for the present backcross study. C57BL/6-backcrossed Vlgr1 knockout mice and 129 (129S1/SvImJ)-backcrossed Vlgr1 knockout mice were established and their phenotypes investigated. Vlgr1 knockout mice showed hearing loss and high susceptibility to audiogenic seizures regardless of their genetic backgrounds. 129-backcrossed Vlgr1 knockout mice exhibited 10-20dB more severe hearing loss than C57BL/6-backcrossed Vlgr1 knockout mice. In general, 129-backcrossed Vlgr1 knockout mice showed a higher incidence of wild running than C57BL/6-backcrossed Vlgr1 knockout mice, and this incidence became smaller as they matured. However, C57BL/6-backcrossed Vlgr1 knockout mice showed a significantly higher mortality rate as a result of auditory stimulation 3 weeks postnatally than 129-backcrossed mice.