Small eye (Pax6Sey) is a semi-dominant mutation affecting development of the eyes, brain and nasal structures. The mutant phenotype arises from defects within the Pax6 gene and several mutant alleles have been identified. A previous study reported that Pax6Sey/Pax6Sey homozygotes, in a random-bred stock, had a median cartilaginous rod-like structure in the nasal region and 80% had supernumerary upper incisor teeth. In this study we show that supernumerary upper incisor teeth and a previously unreported nasal capsule-derived cartilaginous 'spur' occur in compound heterozygous Pax6Sey-Neu/Pax6Sey and homozygous Pax6Sey/Pax6Sey fetuses from several strains of mice. The frequencies of the abnormal phenotypes were not related to allele type but showed variable penetrance, which was dependent on genetic background. The median nasal cartilaginous rod-like structure was present in all homozygous small eye fetuses. The Pax6Sey/Pax6Sey homozygote may provide insight into the complex gene interactions involved in eye, nasal and craniofacial morphogenesis.