Polymerase chain reaction (PCR) and low-stringency single-specific primer PCR (LSSP-PCR) analyses were used to detect Leishmania (Viannia) braziliensis DNA and investigate kDNA signatures of parasite populations present in oral and nasal mucosa lesions from mucosal leishmaniasis patients. A total of 25 samples from 22 patients were processed by specific PCR/hybridization assays. Parasite DNA was detected in all samples analyzed. The intraspecific polymorphism of the variable region of L. (V.) braziliensis kDNA minicircles was also investigated by LSSP-PCR. Similar kDNA signatures were observed in parasites recovered from nasal and oral mucosa lesions of the same patient. In contrast, genetically divergent profiles were detected in lesions from patients biopsied at different times within a period of 1 year. This is the first work to report genetic typing of L. (V.) braziliensis directly from human oral and nasal mucosal lesions.