Arbitrarily primed polymerase chain reaction (AP-PCR) method was applied to the differentiation of clinical isolates of M. tuberculosis strains. The primer which is specific to human papilloma virus (HPV) type 18 was found to be appropriate for the AP-PCR-based differentiation of M. tuberculosis isolates, since AP-PCR produced multiple polymorphic DNA bands when M. tuberculosis DNA was used as template. AP-PCR was performed using either one of the HPV type 18 primer and IS6110-specific primer (half-specific PCR, HS-PCR) or HPV type 18 primer pair only (nonspecific PCR, NS-PCR). The usefulness of these two methods in differentiating M. tuberculosis isolates, was measured by calculating dissimilarity values of 16 isolates using Cluster Analysis software. The highest dissimilarity values by HS-PCR and NS-PCR methods were 0.38 and 0.59, respectively. This suggested that NS-PCR method is better than HS-PCR method in strain differentiation. Although the dissimilarity value calculated by Cluster analysis of the standard restriction fragment length polymorphism method, in which IS6110 was used as a probe, was much more higher than the NS-PCR method, NS-PCR method using HPV 18 primers was quite useful for the differentiation of M. tuberculosis strains due to its rapidity and simplicity.