Seabirds are suitable biomonitors for several persistent organic pollutants (POP), such as polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs), although scarce studies of PAHs in seabirds are available, especially in South American populations. Therefore, this study aimed to assess OCPs, PCBs and PAHs, through gas chromatography-electron capture detector (GC-ECD) and gas chromatography-mass spectrometry (GC-MS) analyses, in liver (n = 9) and muscle tissue (n = 13) from juvenile Magellanic penguins (Spheniscus magellanicus) found stranded on the coast of Rio de Janeiro, Southeastern Brazil. DDT-related compounds were the most frequently detected OCP, and 4,4'-dichlorodiphenyldichloroethylene (DDE), the main DDT metabolite found in penguin tissues. OCP concentrations in liver were two-fold higher than in muscle tissues. Compound specific ratios identified recent exposure of penguins to some OCPs as well as evidence of legacy pollution associated with industrial sources. The predominant PCB congeners were PCB 8/5, PCB 138/160 and PCB 153/132, with concentrations ranging from