We used spoligotyping and restriction fragment length polymorphism (RFLP) of the IS6110-insertion sequence to study the molecular epidemiology of multidrug-resistant (MDR) tuberculosis in Spain. We analyzed 180 Mycobacterium tuberculosis complex isolates collected between January 1998 and December 2000. Consecutive isolates from the same patients (n ؍ 23) always had identical genotypes, meaning that no cases of reinfection occurred. A total of 105 isolates (58.3%) had unique RFLP patterns, whereas 75 isolates (41.7%) were in 20 different RFLP clusters. Characterization of the katG and rpoB genes showed that 14 strains included in the RFLP clusters did not actually cluster. Only 33.8% of the strains isolated were suggestive of MDR transmission, a frequency lower than that for susceptible strains in Spain (46.6%). We found that the Beijing/W genotype, which is prevalent worldwide, was significantly associated with immigrants. The 22 isolates in the largest cluster corresponded to the Mycobacterium bovis strain responsible for two nosocomial MDR outbreaks in Spain.Tuberculosis (TB) remains one of the infectious diseases responsible for the most adult deaths in the world because of the lack of access to effective and rationally delivered therapy for drug-susceptible TB. Spain has one of the highest incidences of TB in Western Europe. The incidences of pulmonary TB were 22.67, 21.05, and 19.64 per 100,000 inhabitants, respectively, in 1998, 1999, and 2000 (29). Standard restriction fragment length polymorphism (RFLP) analysis (30) revealed that 39% of isolates collected in Zaragoza (where the incidence of TB is similar to that in the whole of Spain) in 1993 were clustered (30), suggesting recent transmission. This was recently confirmed by van Deutekom et al. (37). The percentage of clustered isolates increased to 46.6% when the study period was extended to 3 years (13). Multidrug-resistant (MDR) TB is emerging as an increasingly major cause of morbidity and mortality (22). MDR TB outbreaks have been described worldwide (1,2,20,24,27). Highly resistant strains of TB have caused numerous institutional outbreaks (hospitals, prisons, and shelters), with high case-fatality rates among the immunosuppressed and high rates of transmission to immunocompetent health care workers (44). A study with guinea pigs showed that mutations or deletions within the katG gene decrease the pathogenicity of isoniazid (INH)-resistant strains of Mycobacterium tuberculosis (16). A recent study in Los Angeles County showed that the transmission of MDR TB can be limited (7.8%) by aggressive surveillance (21). A recent study in The Netherlands showed that INH-resistant isolates harboring a mutation at amino acid 315 and INH-susceptible strains are equally likely to cluster (40). The precise extent and features of drug-resistant TB in Spain are not known. Incidences of primary MDR TB in 2001 were 0.8% in Barcelona and 1.4% in Galicia (43), suggesting a low incidence of MDR TB in Spain. The transmission of a particular MDR Mycobacterium bovis "B...