The effects that immigration might have on the epidemiology of tuberculosis (TB) in a low-incidence area of Italy was investigated by determining, in autochthonous and immigrant TB patients, the molecular characteristics of the Mycobacterium tuberculosis complex (MTBC) isolates, which may provide information on their phylogeographical origin. A total of 1080 MTBC strains, collected during a 4- year period in Tuscany from 614 Italian-born and 466 foreign-born patients, were genotyped by spoligotyping and assigned to the different phylogeographical lineages that constitute the MTBC. The autochthonous Euro-American phylogeographical lineage, which includes the spoligotype families T, Haarlem, Latin American–Mediterranean (LAM), S and X, was highly prevalent among Italian-born patients, with a total of 477 cases (77.7%), and foreign-born TB patients, with a total of 270 cases (57.9%); 24 Italian-born (3.9%) and 141 foreign- born (30.3%) TB cases were due to MTBC genotypic families associated with distant geographical areas, i.e. East African–Indian (EAI), Beijing, Central Asian (CAS), and Mycobacterium africanum. Strains of Mycobacterium bovis and strains of undefined genotype, which are all considered together, as it is not possible to assign a specific geographical origin, accounted for 113 (18.4%) Italian cases and 55 (11.8%) foreign-born cases. A total of 79 Italian TB cases (12.9%) have been attributed to transmission from immigrants to the local population. No significant contribution to drug resistance appeared to be associated with imported MTBC strains. It is concluded that, at present, the overall impact of imported TB on public health in the low-incidence study area is relatively modest and of the same order as in other western countries.