Population flow between Southeast Asian countries and Japan continues to gather pace. Accordingly, the number of foreigners involved in incidents in Japan has markedly increased, which means that forensic dentistry is now increasingly being faced with the need to analyze DNA from persons of non-Japanese extraction. The DNA test currently used for personal identification mainly utilizes short tandem repeats (STRs) on autosomal chromosomes and the Y-chromosome. This test was developed for use in personal identification, not for distinguishing among races; nonetheless, the standard method for personal identification is often used because the procedure has been established. To determine the degree to which racial differences can be distinguished by standard DNA analysis, 23 STRs located on the Y chromosome were investigated in 218 Malay and 426 Japanese males. The frequencies of each STR were calculated in the two populations. The difference in the power of discrimination between the Malay and Japanese populations ranged from a minimum of 0.01 to a maximum of 0.27; the difference in polymorphic information content ranged from 0.01 (minimum) to 0.23 (maximum). No major differences were noted in the polymorphisms in these two Mongoloid populations, but the distributions of the 17 STRs differed significantly. Short tandem repeat types demonstrating a likelihood of racial differences were identified in 14 of the STRs. Race-specific STR types were identified in 10 STRs. These results suggest that the likelihood of Malay or Japanese genetic background can be judged based on Y-chromosome STR test results.