We carried out a study to investigate the presence of some protozoan parasites (Cryptosporidium sp., Giardia sp., Toxoplasma gondii) on three species of Antarctic penguins: Adélie (Pygoscelis adeliae), gentoo (Pygoscelis papua) and chinstrap (Pygoscelis antarctica) from different locations along the Antarctic Peninsula and the South Shetland Islands. Swabs and faeces samples were analysed by PCR assay for Cryptosporidium sp. and Giardia sp. while Toxoplasma was studied using serological methods from blood samples. We did not detect the presence of these organisms in the species studied. However, based on the upper values of the confidence intervals of the observed prevalence, their presence cannot be completely excluded.