Conservation of species requires knowledge on population changes in time, but achieving such data in proper spatio-temporal scales can often be difficult for rare and vulnerable species. We used long-term (1950–2005) diet data of three avian predators (the nocturnal Ural and eagle owls and the diurnal goshawk) from four landscapes to study population changes of two forest-dwelling species, the Siberian flying squirrel Pteromys volans and the red squirrel Sciurus vulgaris in Finland. We also determined the role of vulnerable flying squirrel in the diet of these predators. Both squirrel species were relatively rare in the diets of the three avian predators, with the exception of red squirrel in the diet of goshawks. The Siberian flying squirrel also appears to be a less important prey for avian predators than flying squirrel species (Glaucomys spp.) are in North American forest communities. Numbers of consumed flying squirrels, but not of red squirrels, increased as the abundances of voles increased in the diets of eagle and Ural owls, that is more flying squirrels were consumed during the good vole years than the poor ones. The declining trends in the diets of three avian predators appeared to be quite similar for both studied squirrel species, possibly indicating that the process behind the decline has been the same.