Recently, selective PCR method using DT1 and DT6 sequences was introduced to identify and differentiate the Mycobacterium avium complex (MAC) into M intracellulare and M. avium. We applied this method to 49 MAC clinical isolates identified by biochemical tests. They were differentiated into 39 strains of M. intracelluare and 10 strains of M. avium. Compared to those results obtained by 16S rDNA sequencing, DT1-DT6 PCR method showed 100% specificity. While the sensitivity of DT6 PCR for M. avium was 100%, that of DT1 PCR for M. intracellulare was 84.6%. These results show heterogeneity of M. intracellulare Korea clinical isolates from Korea. In conclusion, although the in-house DT1-DT6 PCR is an easy and convenient method in differentiating MAC members, other methods such as 16S rDNA sequencing analysis should be performed for the correct identification, especially of M intracellulare.