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Histoplasma capsulatum was isolated from gut, lung, liver, and spleen of 17 of 208 captured bats belonging to 6 different genera and species. Three of the 17 infected bats were from the State of Guerrero and 14 were from the State of Morelos. All were adult bats: 6 males (1 Pteronotus parnellii, 2 Natalus stramineus, 2 Artibeus hirsutus, and 1 Leptonycteris nivalis) and 11 females (1 Myotis californicus, 1 Mormoops megalophylla, 8 A. hirsutus, and 1 L. nivalis). High rates of bat infection with H. capsulatum were found in the monitored sites of the State of Morelos. Histoplasma infection of N. stramineus, A. hirsutus, and L. nivalis should be considered as the first records in the world. The fungus isolated from infected bats was identified by its typical mycelial-phase morphology and by its yeast-phase conversion. Exoantigen production confirmed the fungal identification by the presence of specific precipitation lines in double immunodiffusion assays using human immune serum. Histopathologic studies showed intracellular yeast-like cells compatible with H. capsulatum yeast-phase in tissues of several bats, especially in pulmonary (intra-alveolar and septal) macrophages, with none or minimal tissue reaction. In contrast to past reports, present data support a high risk of bat infection with H. capsulatum in Mexican cave environments.