<p>Populations of raptors in Europe recovered at the end of twentieth century from heavy decline due to contaminants and persecution in the past, however, some species or populations in certain regions continue to face pressure from human induced mortality today. Causes of mortality may vary between raptor species, sexes, age groups, and seasonally throughout the year. Therefore, it is important to understand reasons and patterns for mortality in a particular region because knowledge derived from elsewhere may not be applicable for the target populations. We studied mortality patterns in White-tailed Eagle (<i>Haliaeetus albicilla</i>; <i>n</i> = 94) and Osprey (<i>Pandion haliaetus</i>; <i>n</i> = 45) in the eastern region of the Baltic Sea, Lithuania. Most deaths were human related for both species with the majority caused by electrocution, but even more frequent for Osprey than White-tailed Eagle. For both species, the pattern of mortality differed between young and adult birds, but in opposite ways. However, there was no evidence of differences between sexes or seasons. White-tailed Eagles death recoveries were spatially aggregated with several notable hotspots, but deaths of Ospreys were randomly distributed throughout the region. Despite association of both raptors with aquatic habitats, most likely, species-specific mortality patterns emerged because of behavioural and life history differences. Our results suggest that conservation efforts should be focused on understanding and dealing with the main threats for the species, but also could benefit from prioritisation of efforts in most problematic areas for raptor species if the clustered mortality pattern is evident.</p>