A genotype of JC virus (JCV) DNA extracted from human urine can serve not only as a means of elucidating human migration patterns, but also of tracing the origin of unidentified cadavers. If a JCV genotype is determined using a small amount of urine or urine stain from a given person, it may be useful in identifying the geographic area in which that person was born. In the present study, we amplified a 610-bp intergenic region (IG region) of JCV DNA extracted from 200 μl of each of 82 urine samples collected in Japan. JCV DNA was detected in 45 of 82 urine samples (54.9%) and genotypes were also determined by restriction fragment length polymorphism analysis (MY genotype: 13; X (CY) genotype: 25; unclear: 7). Additionally, 16 urine stains which had been prepared 3 months earlier using 100 μl of JCV-positive urine were examined. JCV DNA was detected in 11 of 16 urine stains (68.8%), and in this case also, it was possible to determine the genotype by the phylogenetic analysis after DNA sequencing.   The present study indicates that JCV genotyping can be successfully conducted using only 100 μl urine stain and even 3 months after the urine stain was made. Thus, JCV genotyping shows promise as a new analytical method for narrowing down the native place of unidentified persons or cadavers from urine stains left at the scene.