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Within continental waters, large lakes present a special interest for monitoring persistent contaminants, because of their physical characteristics, particularly a prolonged residence time. Moreover, professional fisheries take place in these large lakes, entailing human exposure to chemicals bioaccumulated. For these reasons it has long been acknowledged that monitoring persistent contaminants in fish is an essential component of environmental and health risk assessment in such large lakes. We report data on fish contamination by a range of perfluoroalkyl substances for seven European deep lakes located in populated areas, namely Lake Geneva, Lake Lugano and Lake Maggiore (all three being trans-national lakes), and Lake Iseo, Lake Como, Lake Garda and Lake Mergozzo in Italy. In addition, fish from two high altitude alpine lakes in Switzerland (>2000 m) were also sampled. These high altitude lakes were assumed to be references sites, as only atmospheric deposition should bring PFAS to them. All the other lakes are located in highly urbanized areas but without known industrial PFAS sources. A range of perfluorocarboxylic and perfluorosulfonic acids were analyzed in fillets from seven fish species occupying different habitats. Furthermore, in order to be able to assess wildlife as well as human exposure, different body fractions were analyzed separately in selected cases. Along with a summary of the results (in terms of concentration ranges and descriptive statistics), we will provide insights on the effect of seasons or type of PFAS source, and discuss about the relationships between concentrations in fillets and whole-fish.