Leishmaniasis is a parasitic infection transmitted by the bite of infected female sandflies. It principally affects the skin, and the frequency of mucosal involvement is about 5% to 20%. Considering the rarity of leishmaniasis affecting the upper aerodigestive tract mucosa, we evaluated the characteristics of mucocutaneous leishmaniasis and mucosal leishmaniasis and the diagnostic difficulty when the parasites are scarce in tissue samples. The clinical, histopathological, histochemical, immunohistochemical, and molecular features of 17 cases of mucocutaneous leishmaniasis and mucosal leishmaniasis were assessed. Mucosal disease was principally found in the soft palate, oropharynx, and nose, manifesting mainly as a solitary ulcer. In hematoxylin and eosin–stained sections, 10 cases revealed abundant amastigotes within the macrophages. Giemsa staining was not shown to be helpful to confirm the diagnosis in 6 cases with scarce or nondetectable amastigotes. Immunohistochemistry (IHC) showed high sensitivity by positive staining in 14 out of 17 cases (82.3%). Polymerase chain reaction was shown to be more sensitive than IHC with 13 out of 14 (92.8%) positive cases, including the 3 IHC negative cases; however, this technique is not available in many endemic regions. In summary, we suggest that the IHC is a simple technique with rapid results and relatively low cost, when compared with other laboratorial procedures; thus, IHC is a helpful tool that should be implemented in the routine diagnosis of leishmania.