SETTING: Predominant genotypes of Mycobacterium tuberculosis include the Beijing family, which has caused large tuberculosis outbreaks and has been associated with increased virulence and multidrug resistance (MDR). OBJECTIVE: To search for the Beijing genotype among Latvian MDR patients to characterise their DNA isolates at the molecular level. DESIGN: MDR isolates were spoligotyped and tested for gene mutations by automatic nucleotide sequencing. RESULTS: Of 109 isolates examined, 95 were located in six clusters of 2 to 63 isolates each. The 63 isolates in the largest cluster had an identical pattern corresponding to the Beijing genotype. The remaining isolates were of a non-Beijing genotype and formed another large group whose similarity ranged from 72% to 100%. Mutations in the rpoB and katG genes were compared in the Beijing and non-Beijing strains. In both groups, the rpoB gene mutations predominated in codons S531L (52.2%) and D516V (14.7%). Double mutations in the rpoB gene were observed in 8.2% of the isolates, most of them located among Beijing-type isolates. The katG gene mutation S315T (98.4%) was prevalent among all isolates. CONCLUSION: Molecular analysis of MDR isolates of M. tuberculosis demonstrates that the Beijing genotype, most likely due to recent transmission, is prevalent in Latvia among MDR patients and that this genotype can be associated with double mutations.