Abstract Avian malaria is one of the most important diseases of captive penguins. We employed morphometric techniques to evaluate hepatic hemosiderosis in rehabilitating wild Magellanic penguins (Spheniscus magellanicus) that were negative (n = 9) or naturally infected by different subgenera of Plasmodium spp. (n = 24), according with: Plasmodium subgenera (Haemamoeba, Huffia, Other lineages, and Unidentified lineages), severity of Plasmodium histopathological lesions, and concurrent diseases, age class (juvenile or adult plumage), sex (male, female or not determined), body score (emaciated, thin, good, excellent, not available), molt, presence or absence of oil contamination upon admission, iron supplementation, and rehabilitation center. The percentage of the area occupied by hemosiderin was called ‘Index of Hepatic Hemosiderosis (IHH)’. Plasmodium-positive females presented significantly higher IHH values (17.53 ± 12.95%) than males (7.20 ± 4.25%; p = 0.041). We observed higher levels of congestion (p = 0.0182) and pneumonia (p = 0.0250) severity between Unidentified lineages vs. Huffia. We believe that the hepatic hemosiderosis observed in this study was multifactorial, the result of pathological processes caused by malaria, molting, hemoglobin and myoglobin catabolism during migration, anemia, concomitant diseases, and iron supplementation, all possibly potentiated by decreased liver mass. Further studies are needed to clarify the mechanisms of these hypotheses.