Basal cell nevus syndrome (BCNS; also nevoid basal cell carcinoma syndrome [NBCCS]; Gorlin's syndrome) is an autosomal dominant syndrome characterized by multiple basal cell carcinomas, keratocysts, and developmental skeletal defects. Mutation of the human homologue of Drosophila patched (PTC) gene is considered to be the molecular defect in BCNS. PTC mutations have been observed in sporadic tumors including basal cell and ovarian carcinomas and medulloblastoma. The authors report a novel C/T polymorphism in the PTC gene. Forty-eight normal blood samples were screened for the presence of the polymorphism using direct radioactive and automated sequencing of polymerase chain reaction (PCR) products and restriction enzyme digestion. Results demonstrated 20 homozygous T (43%), 11 homozygous C (23%), and 17 heterozygous C/T (35%). The presence of this polymorphism has permitted us to directly detect allelic loss in BCNS, sporadic keratocysts, and basal cell carcinoma (BCC). Further, four BCNS keratocysts and two BCNS-BCC and three non-BCNS keratocysts showed allelic loss of complementary DNA from lesions when compared with their corresponding blood genomic DNA.