In Mycobacterium tuberculosis there is a strong correlation between in-vitro resistance to rifampicin (RIF) and pyrazinamide (PZA) and mutations in rpoB and pncA, respectively. Approximately 50 mutations associated with resistance have been reported for rpoB and 70 for pncA, and, theoretically, many more are possible. Therefore, the identification of rpoB and pncA mutations in M. tuberculosis might be used for the simultaneous determination of resistance and for typing multi-drug-resistant (MDR) strains during possible outbreaks. The present study examined four sensitive and six MDR isolates of M. tuberculosis from Turkey and eight isolates from a nosocomial MDR tuberculosis (TB) outbreak in the UK. Gene mutations were identified by the Innogenetics LiPA rpoB assay or automated sequencing, or both. All the sensitive isolates had rpoB and pncA wild-type genotypes, whereas all the RIF- and PZA-resistant isolates had rpoB and pncA mutations. All four mutations seen in rpoB, but none of the six in pncA, had been reported previously. The rpoB and pncA mutations seen in the Turkish isolates defined six distinct genotypes amongst the six MDR isolates, while standard IS6110 typing discriminated only four. All isolates from the single strain MDR-TB outbreak had identical genotypes. Rapid genotyping was performed on the sputum from a patient who presented 2 years after the initial MDR-TB outbreak and this showed rpoB and pncA genotypes identical to the other outbreak isolates. This result was available within 36 h. The analysis of rpoB and pncA is a rapid and practical means of simultaneously identifying and typing MDR isolates of M. tuberculosis.