Background: Traditional methods for the diagnosis of leishmaniasis yield poor sensitivity, which limits its effectiveness in lesions with a low parasite burden. Methods: Retrospective pathologic study of 360 cases of cutaneous leishmaniasis and analysis of the different diagnostic methods used. Results: In 93% of the lesions, histopathology showed a dense and diffuse inflammatory infiltrate, consisting of lymphocytes, histiocytes and plasma cells, which occupied the superficial and mid dermis and variably extended to deep dermis and superficial subcutis (standard pattern). The remaining cases exhibited atypical features, such as perivascular, interstitial or perifollicular inflammatory patterns, folliculitis or panniculitis. Granulomas were identified in 84% of biopsies, most of them as small, poorly formed, non-necrotizing histiocytic aggregates. Amastigotes were visualized by routine histopathologic exam in 36% of biopsies. Immunohistochemistry stained 17 of 26 lesions (65%) negative by conventional stains. PCR provided the correct diagnosis in 218 cases (58% of the series) negative for Leishmania by other techniques. Conclusions: Biopsies negative for Leishmania by traditional diagnostic methods that show the histopathologic standard pattern, those with atypical features from patients with clinical suspicion of cutaneous leishmaniasis in endemic areas, should be studied by immunohistochemistry and/or PCR for Leishmania in order to reach the definitive diagnosis.