Leishmania (Viannia) braziliensis is the main etiological agent of cutaneous and mucocutaneous leishmaniasis in Latin America. Reports have described non-ulcerated atypical tegumentary leishmaniasis cases caused by L. braziliensis in several regions of the world, including in patients from the Xacriabá Indigenous reserve, in São João das Missões/Minas Gerais - Brazil. Parasites isolated from these atypical clinical lesions have previously been found to be resistant to antimony-based therapeutics. In the present study, proteins displaying differential abundance in 2 strains of L. braziliensis isolated from patients with atypical lesions compared with 4 strains isolated from patients with typical lesions were identified using a quantitative proteomics approach based on tandem mass tag labeling (TMT) and mass spectrometry. A total of 532 (p value <0.05) differentially abundant proteins were identified (298 up-regulated and 234 down-regulated) in strains from atypical lesions compared to strains from typical lesions. We observed a variety of proteins with differential abundance among the studied strains. Prominent positively regulated in atypical strains included proteins which may confer a greater survival inside the macrophage, proteins related to resistance to antimony and higher peroxidase activity. Also were identified proteins suggest as new drug and vaccines target. Our data contribute to characterization of these intriguing L. braziliensis strains, and sheds new light on ACL cases has been associated with therapeutic failures.