HIV-1 infection and HIV-1-induced immune deficiency may play a role in selecting particular Mycobacterium tuberculosis (MTB) strains (i.e. genotypes). We compared 43 MTB isolates obtained from HIV-1-infected patients with 77 MTB isolates obtained from HIV-1-uninfected patients in Burkina Faso, by means of DNA fingerprinting methods (MIRU-VNTR plus spoligotyping). This study suggests a lack of structure of the MTB population caused by HIV-1 infection and a similar genetic diversity of MTB in HIV-1-infected compared with uninfected individuals.