This study investigates whether differences in urinary odors of two major histocompatibility complex (MHC) congenic strains of mice reared in germfree conditions could be detected by male Sprague-Dawley rats in a habituation-dishabituation procedure. Rats were tested for their ability to discriminate between urine odors from one of the following pairs: (a) MHC congenic mice (B6 and B6-H-2k) housed in conventional conditions; (b) MHC congenic mice (B6 and B6-H-2k) raised in a germfree environment; (c) genetically identical mice maintained in conventional housing; or (d) genetically identical mice raised in a germfree environment. The urine odors of mice from the two MHC congenic strains raised in conventional housing were discriminable, but the urine odors of MHC congenic mice raised in a germfree environment were not discriminable. The odors of genetically identical mice, whether housed conventionally or under germfree conditions, were not discriminable. These results indicate that germfree rearing influences the urinary odors of individuality in MHC congenic mice. We discuss the possibility that the disparate findings from previous studies are a result of the methodologies employed.