JC polyomavirus (JCV) is ubiquitous in humans, persisting in renal tissue and excreting progeny in urine. It has been shown that the genotyping of urinary JCV offers a novel means of tracing human migrations. This approach was used to elucidate the racial composition of modern China. JCV isolates in the Old World were previously classified into nine distinct genotypes. One of them (B1) has a wide domain, encompassing part of Europe and the entirety of Asia. By constructing a neighbour-joining phylogenetic tree, all B1 isolates detected so far were classified into four distinct groups (B1-a to -d), each occupying unique domains in the world. According to this revised classification system of JCV DNAs, four genotypes (CY, SC, B1-a and -b) were found to be prevalent in China and Mongolia (Mongolia was studied instead of Inner Mongolia, which is part of China). There was a remarkable variation in the incidence of genotypes among the sites of sample collection. CY was more frequently detected in Northern China, SC was predominant in Southern China and B1-b was detected only in Mongolia. B1-a was spread throughout China. These data were statistically analysed and the observed regional differences in the incidence of genotypes were found to be significant. It is likely that these differences in JCV distribution in China reflect the intermingling of different population groups that constitute modern China.