This study evaluates the positivity of Mycobacterium leprae DNA in the nasal secretion (NS) of patients with leprosy and healthy individuals; and the genetic variability between strains of M. leprae, studying the relationship with clinical and epidemiological factors. NHS samples were analyzed from 185 patients, 136 individuals without leprosy who attended the Dona Libânia National Reference Center for Sanitary Dermatology in Fortaleza, Ceará and 121 students from the Christus College in Fortaleza. Skin biopsies (SB) from 38 patients were analyzed. All SN samples were subjected to amplification of the RLEP region using NESTED PCR. To assess the genetic diversity of M. leprae between individuals, SN strains from 48 RLEP-positive patients were analyzed using four variable number tandem repeat loci (VNTRs). To study the variability of the strain in the same individual, BP and SN samples from 38 positive patients in the RLEP system were compared using the 15 VNTR loci.