Objective The CL/Fr mouse, known as a strain with spontaneous cleft lip and/or palate (CL/P), has been used as an animal model to investigate etiology in CL/P. Method We examined a facial asymmetry mutant discovered in a CL/Fr mouse colony that was not associated with CL/P and was shown to be inheritable in subsequent generations. Facial asymmetry became apparent with postnatal growth, whereas it was not detectable at birth, and was termed “maxillary bending” (MB) based on the characteristic bending of the maxilla. Results As a result of selective breeding, an ‘MB line,’ in which MB was observed in 21.68% (67/309) in addition to CL/P in 17.80% (55/309) of the offspring, was developed in the CL/Fr colony. In mating experiments between the MB line and C57BL/6J, all F1 progeny showed the normal phenotype. MB was observed In 0.72% (1/139) of the F2 generation, and the backcross generation showed segregation of MB in 6.25% (22/352) and CL/P in 1.42% (5/352). These instances suggested the occurrence of an additional mutation in the CL/Fr mouse genome controlled by an autosomal recessive gene with low penetrance. However, since the CL/Fr mouse primarily has a developmental deficiency in the maxilla, the possibility that CL/P and MB share common etiologic factors cannot be completely ruled out. Conclusion The maxillary bending retains significance, as this mutant can serve as an animal model of abnormal facial growth. Elucidation of the etiologic relationship between MB and CL/P may provide clues to clarifying the deficiency in first branchial arch In the mouse.