The aim of marine animal rehabilitation centres is to receive, screen and rehabilitate marine species so that they can be reintroduced to their natural habitat. Aquatic species, especially migratory ones, suffer intense environmental pressures caused by anthropogenic actions in their breeding and feeding grounds. Species are often found stranded on beaches in a critical state of health or even dead, mainly due to ocean pollution. Magellanic penguins are the most common migratory seabirds in rehabilitation centres on the south-west Atlantic coast. During migration, many young birds end up lost and stranded on the Brazilian coast. Viral, bacterial and fungal diseases, as well as parasites, can complicate the penguins' recovery and even cause their death. Most of the time, these diseases are contracted on the premises of rehabilitation centres. The aim of this study was therefore to describe the main difficulties encountered in these centres and in the treatment of diseases in Magellanic penguins.