Aspergillosis, an opportunistic mycosis caused by the Aspergillus genus, affects mainly the respiratory system and is considered one of the most significant causes of mortality in captive penguins. This study aimed to examine a 6-yr period of cases of aspergillosis in penguins at the Centro de Recuperação de Animais Marinhos (CRAM-FURG), Rio Grande, Brazil. A retrospective cohort study was conducted using the institution's records of penguins received from January 2004 to December 2009. Animals were categorized according to the outcome “aspergillosis,” and analyzed by age group, sex, oil fouling, origin, prophylactic administration of itraconazole, period in captivity, body mass, hematocrit, and total plasma proteins. A total of 327 Magellanic penguins (Spheniscus magellanicus) was studied, 66 of which died of aspergillosis. Proportionate mortality by aspergillosis was 48.5%, and incidence density was 7.3 lethal aspergillosis cases per 100 penguins/mo. Approximately 75% of the aspergillosis cases occurred in penguins that had been transferred from other rehabilitation centers, and this was considered a significant risk factor for the disease. Significant differences were also observed between the groups in regard to the period of time spent in captivity until death, hematocrit and total plasma proteins upon admission to the center, and body mass gain during the period in captivity. The findings demonstrate the negative impacts of aspergillosis on the rehabilitation of Magellanic penguins, with a high incidence density and substantial mortality.