The increasing Baltic grey seal (Halichoerus grypus) population causes considerable damage to coastal fisheries. The aim of the present study was to compare the age, sex and blubber thickness of seals that cause problems to coastal fisheries (i.e. by-catch seals and those shot near the fishing gear) with those killed during regular hunting. This knowledge is essential for population management. We collected seal samples from hunters and fishermen from Finland, Sweden and Estonia in 2011–2013. Hunted seals included individuals of all age classes, whereas most by-catch seals were small pups (in spring) or sub-adult and adult males (in autumn). By-catch seals had a thinner blubber layer than hunted seals. Most seals shot near the fishing gear were adult males in good condition. The ‘problem seals' were thus not a random sample of the population. We suggest that hunting should be targeted especially at males to mitigate the damage to fisheries without threatening the population.