Although basal cell carcinoma (BCC) is a major skin cancer, the mechanism of carcinogenesis with regard to cytogenetic abnormalities has not been fully investigated. In the present study, we carried out cytogenetic analyses of 18 patients (9 male and 9 female) with BCC. Aneuploidy was seen by Q-banding method in more than half of the cases and was mostly loss of the sex chromosome. We also performed FISH to the interphase nuclei of various tissues and short-term cultured BCC cells. The frequency of sex chromosomal aneuploidy was significantly higher in all samples from BCC patients (peripheral blood lymphocytes, non-lesional tissues, BCC tumor tissues and cultured BCC cells) than in age-matched normal controls. In addition, we analyzed clonality of BCC tissues using a human androgen receptor gene assay and found uniparental pattern of inactive X-chromosomes. This indicates that BCC cells were monoclonal in origin and the development of BCC might be correlated with sex chromosomal aneuploidy, which acquired accumulation of genetic mutations.