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Congenital malformations (CMs) or developmental abnormalities are pathological processes defined as morphological defects that originate during embryonic stages. A wide variety of CMs is observed in reptiles, most of which are incompatible with normal life. Characterization of CMs and their pathogenesis are of great importance for the conservation of reptiles, including neotropical viperids (NVs). External CMs are often reported in these species, but little is known about concomitant microscopical findings in the viscera of malformed individuals. In order to partially fill in this gap in knowledge, we aimed to investigate and characterize histopathological findings in the viscera of malformed NVs, jararacas (Bothrops jararaca) and South American rattlesnakes (Crotalus durissus), correlating these findings with features of external CMs. From 78 malformed snakes analysed, 100% (19/19) of rattlesnakes and 98.3% (58/59) of jararacas had histopathological changes in the viscera. Liver and/or kidney fatty degeneration was the most common finding in malformed and control animals. Renal glomerulocystic and tubular disease was significantly correlated with brachygnathia (P < 0.05) in jararacas. These results add to the body of knowledge of snake pathology and demonstrate some associations between external CMs and visceral histopathological findings, some of which could have implications for individual survival., (Copyright © 2018 Elsevier Ltd. All rights reserved.)