The goal of the present study was to examine the transmission dynamics of multidrug-resistant tuberculosis (MDR-TB) in Switzerland. Between 2006 and 2012, a total of 49 MDR-TB cases were reported to the Swiss Federal Office of Public Health, 46 of which were of foreign origin. All 49 initial strains were evaluated by molecular epidemiologic methods at the Swiss National Reference Centre for Mycobacteria. In 43 strains, unique DNA fingerprint patterns were identified. Twelve strains were grouped into six clusters. Data from contact tracing suggest likely in-country transmission in four clusters, mostly among close contacts. In the remaining two clusters, no contact tracing data were available, but the identified genotypes were known to be prevalent in the countries of origin of the patients, suggesting the possibility that the infection was acquired there. While most MDR-TB cases are imported to Switzerland, at least four of the 49 MDR-TB cases were due to transmission within the country. The imported cases, however, did not lead to secondary cases outside the circles of close contacts. The results also indicate that prevention of MDR-TB transmission among immigrants may require closer monitoring.