The knowledge of raptor pathogens and associated lesions may be extremely important to enhancing raptor conservation efforts and reducing pathogen spillover to humans and domesticated animals and vice versa. Parasite infections of the digestive system and associated bacteria and pathological changes were evaluated in deceased diurnal and nocturnal raptors in central Italy. Overall, the prevalence of parasites (nematodes, cestodes, trematodes, acanthocephalans, and protozoa) identified in the examined birds was 72.41%, and most of the positive raptors (71.42%) showed multiple parasite infections. Among bacteria, Salmonella typhimurium, Salmonella enterica subspecies diarizonae, Escherichia coli, Clostridium perfringens, Yersinia enterocolitica, and Pasteurella multocida were identified. The results obtained showed that both parasites and bacteria may cause severe lesions in the digestive system of diurnal and nocturnal raptors; parasites and bacteria may concur in causing these lesions; most severe lesions are caused by the interaction of multiple pathogens, both parasites and bacteria; and the same pathogen taxa are frequently associated with the same pathological changes. This study is the first report of S. typhimurium and S. enterica subspecies diarizonae in Buteo buteo, while Andracantha mergi, Spirocerca spp., Sarcocystis dispersa, Sarcocystis columbae, and Eumonospora spp. were recorded for the first time in Italy.