We evaluated the relationship between rifampin (RIF) susceptiblility and amino acid substitution in rpoB gene of Mycobacterium tuberculosis and the usefulness of rpoB gene sequencing in the rapid prediction of RIF susceptibility of M. tuberculosis in clinical specimens. A total of 76 genetic alterations in the 69 bp core region of rpoB gene were detected in 74 of 130 M. tuberculosis strains. Examination of the correlation between the minimum inhibitory concentrations (MICs) of RIF and amino acid substitutions in the 69 bp core region of rpoB gene revealed that all 43 strains containing amino acid substitution with Leu or Trp in codon 531 showed RIF-resistant phenotypes, with MICs > or = 64 microg/ml. In contrast, a variable level of RIF susceptibility was observed among strains containing amino acid substitutions in either codon 516 or codon 526. In the clinical study, we tested 26 sputum samples, two gastric lavages, and one synovial fluid sample obtained from patients with tuberculosis. The RIF susceptibility predicted by direct rpoB sequencing was satisfactorily compatible with the results of the RIF-susceptibility test and the MICs of RIF against isolated organisms. Our results suggest that rpoB gene sequencing is useful for the detection of M. tuberculosis in clinical samples as well as the rapid prediction of RIF susceptibility of these strains.