To date, only limited results on the fatty composition in different tissues of the top predators in the Baltic Sea are available. In the current study, tissue samples of blubber, skeletal muscle, and liver from 8 harbour porpoise (Phocoena phocoena) and 17 grey seals (Halichoerus grypus) in the Baltic Sea off Mecklenburg-Western Pomerania were included in the investigation. While the total fatty acid content in liver and blubber tissue revealed no differences between both species, the total fatty acid content of muscle tissue was significantly differentand showed higher concentrations in harbour porpoise muscle compared with grey seals. The most abundant fatty acids in the blubber of grey seals and harbour porpoises (18:1cis-9, 16:1cis-9, 16:0 and 22:6n-3) were present in similar quantities and ratios to each other as known from other marine top predators. If future studies can show that differences in tissue fatty acid content are caused by variation in the nutritional status, and this may lead to the development of a more objective assessment of body condition in seals and porpoises recovered via stranding schemes.