A crucial first step in assessing and managing the role and impacts of predators on their environment is knowledge on their foraging behaviour and diet. Here, we synthesize previously published and newly generated data on the diet of harbour seals, grey seals, and ringed seals in the Baltic Sea region. More than 45 000 otoliths recovered from 3147 samples of scats and digestive tracts were collected throughout all seasons and most Baltic Sea sub-basins from 1968 to 2013. The data revealed a large extent of interspecific, spatial, and seasonal variation in seal diet, implying that caution should be made when extrapolating from one species, area or season, to others. Still, a few fish species, including Atlantic herring, sprat, cod, and sandeels had high occurrence across seal species and locations. The compiled data provide the first overview of seal diet across the entire Baltic Sea region, but also comes with several limitations. Thus, while the data presented here constitutes an important reference for future inference, it also illustrates an urgent need for standardizing methodology across studies on the diet of seals and other aquatic predators.