BACKGROUND: Rapid and accurate identification of Mycobacterium tuberculosis complex is important in the diagnosis, treatment, and assessment of prognosis of tuberculosis. But, the conventional identification procedures such as niacin test usually requires considerable time. In this study, we compared the diagnostic value of a gene probe method with that of the niacin test for the differentiation of M. tuberculosis complex from mycobacteria other than tuberculosis (MOTT). METHODS: Commercially available gene probe kit(AccuProbeTM, Gen-Probe, Inc. , San Diego, Calif.) and Niacin test strip were used to identify 78 strains of mycobacteria isolated from patients at Asan Medical Center. One ATCC strain (M. tuberculosis complex) and one MOTT strain were used as controls. Polymerase chain reaction(PCR) was used when the above two tests yielded discordant results. RESULTS: Fifty isolates were identified as M. tuberculosis complex by both gene probe method and niacin test. Likewise 25 isolates were identified as MOTT by the both methods. For the remaining 5 isolates, the results of the two tests differed from each other: M. tuberculosis complex by gene probe and MOTT by niacin test. By PCR, however. these strains were identified as M. tuberculosis. The time required for identification was 1 to 2 hours by gene probe method and 1 to 3 weeks by niacin test. CONCLUSION: Gene probe is simple, rapid and reliable and is a very practical diagnostic tool that can be used in any clinical laboratory.