The paired box 6 (PAX6) is a transcription factor expressed early in development, predominantly in the eye, brain and pancreas. Mutations in PAX6 are responsible for eye abnormalities including aniridia, and it is also known that some PAX6 mutations result in autism with incomplete penetrance. We resequenced all the exons and flanking introns of PAX6 in 285 autistic patients in the Japanese, with the possibility that novel mutations may underlie autism. Fifteen different polymorphisms were identified: 13 are novel, and 2 were previously reported (rs667773 and rs3026393). Among the novel ones, there is one missense mutation that was found in a patient: 136C>G (Leu46Val) (single nucleotide polymorphism ID "ss130452457" is temporarily assigned). Leu46 is extremely conserved from fly to human, and we did not detect Val46 in 2120 nonautistic subjects. The autistic patient carrying this heterozygous mutation showed reduced vision, photophobia and eyelid ptosis, but no other ocular abnormality such as aniridia. Our findings suggest the necessity of further studies on the causal relationship between PAX6 and autism.