The monoclonality of human colonic crypts was demonstrated by human androgen receptor (HUMARA) gene assay following application of the crypt isolation method. DNA was extracted from an isolated single crypt, Hpa II digestion was performed before polymerase chain reaction (PCR) by primers spanning the HUMARA exon 1 region. The PCR product of a single crypt clearly showed allelic exclusion based on methylation status, while PCR product from a mixture of 40 crypts or colonic mucosa as a whole that included epitheliums and interstitial connective tissue had two bands. This method will facilitate the non-isotopic analysis not only of tumor clonality, but also of the normal structures derived from a single progenitor cell.