In total, 48 Mycobacterium tuberculosis clinical isolates from 48 patients with drug-resistant pulmonary tuberculosis (TB) in central Poland during 2004 were analysed by spoligotyping and IS6110-Mtb1/Mtb2 PCR. Twelve (25%) isolates were clustered by spoligotyping in combination with IS6110-Mtb1/Mtb2 PCR. Patients from whom these isolates were obtained were assumed to have developed TB as a result of recent transmission. Spoligotyping, used alone, overestimated the number of clustered isolates. However, combined use of spoligotyping and IS6110-Mtb1/Mtb2 PCR was an efficient approach for revealing clonal relatedness among M. tuberculosis isolates.