Pyogranulomatous lesions from 80 dogs with sporotrichosis and 26 dogs with American tegumentary leishmaniasis (ATL) were compared microscopically in order to identify features that would support the diagnostic suspicion and direct the subsequent search for the aetiological agent of either infection. Odds ratios and their respective 95% confidence intervals were calculated in order to evaluate the impact of the microscopical findings on the diagnosis of either disease. Lesions with well-formed granulomata were 14 times more likely to be due to sporotrichosis than ATL. Marked neutrophil infiltration into granulomata was 12.26 times more likely to be associated with sporotrichosis when compared with lesions having mild neutrophilic infiltration. Absence of lymphocytes and macrophages in the peripheral infiltrate was associated with a 9.71 and 4.93 higher chance, respectively, of being sporotrichosis rather than ATL compared with lesions where these cells were present. Lesions with a perivascular, perifollicular and interstitial peripheral inflammatory infiltrate were 5.48 times more likely to be due to sporotrichosis than ATL when compared with lesions with a diffuse peripheral infiltrate. Histopathological analysis may therefore contribute to the diagnosis of sporotrichosis or ATL skin lesions in dogs since this method permits the identification of features that direct the diagnostic suspicion, thus facilitating the search for the aetiological agent in histological sections, permitting the precise request of subsequent tests and thereby reducing costs and time taken to achieve a definitive diagnosis and the initiation of appropriate therapy.