The genetic polymorphism of Leishmania (Viannia) braziliensis detected in cases of mucosal leishmaniasis (ML) from HIV-infected and non HIV-infected patients was evaluated. Nine samples from three HIV-infected patients and five samples from five non HIV-infected patients were analysed by polymerase chain reaction (PCR), low-stringency single-specific primer PCR (LSSP-PCR) and phenetic analysis. The presence of L. (V.) braziliensis DNA was detected in all samples by specific PCR assay. The intraspecific polymorphism of the variable region of L. (V.) braziliensis kDNA minicircles was investigated by LSSP-PCR. Phenetic analysis grouped the genetic profiles into two distinct clusters, which discriminated between samples obtained from HIV-infected and non HIV-infected patients. In two HIV-infected patients, identical genetic profiles were detected in lesions biopsied at different times after the treatment of the initial lesion. Interestingly, genetically divergent profiles were detected in the cutaneous and mucosal lesions of the same HIV-infected patient collected at the same time. This is the first work comparing genetic polymorphism of L. (V.) braziliensis in cases of mucosal leishmaniasis from HIV-infected and non HIV-infected patients.