Many diurnal raptors are vulnerable to modern forestry and areas surrounding individual raptor nests are often strictly protected. This study compared random forest plots and nest sites of five species of forest-dwelling raptors in Estonia to explore whether timber harvesting per se reduces the probability of raptor nesting when controlling for the effect of nest tree availability and stand structure. Medium-sized species – the honey buzzard (Pernis apivorus), goshawk (Accipiter gentilis), common buzzard (Buteo buteo) and lesser spotted eagle (Aquila pomarina) – preferred natural to managed forests but the preference, when controlling for other stand characteristics, was not significantly related to the incidence of cutting. Instead, the presence of nests depended on structural features of old growth, even for the sparrowhawk (Accipiter nisus), which preferred young secondary forests. The sparrowhawk was the only species for which thinning had an independently negative influence on nest presence. The results stress the importance of structural diversity of forest stands in multiple-use forestry and indicate that if natural stand structure is preserved and disturbance avoided in buffer zones around the nests of medium-sized raptors, some non-commercial cutting (firewood collecting, sanitary cutting) may be allowed there outside the breeding season.