Abstract Haemosporidians, a group of vector-borne parasites that parasitize the blood cells and internal organs of various animal species, are reported to cause severe pathology in raptors. Species belonging to the genera Plasmodium, Haemoproteus and Leucocytozoon are the ones of greatest wildlife importance. The common buzzard (Buteo buteo) and the Eurasian sparrowhawk (Accipiter nisus) are the most numerous raptor species in Europe. Reliable data is lacking for many raptor species in Greece. The aim of this study was to assess, for the first time, the prevalence and geographical distribution of haemosporidian infection (mainly Leucocytozoon and Plasmodium) in these two avian species in Greece, in correlation with the risk factors of age and sex. In total, 62 common buzzards and 26 Eurasian sparrowhawks were included in this study, all being admitted for treatment at a Greek Wildlife Rehabilitation Center. Blood samples were collected and microscopical analysis was performed after staining blood smears with Giemsa. DNA was extracted from each sample and a fraction of the mitochondrial cytochrome b gene was amplified by a nested PCR protocol. All positive samples were subjected to sequencing. Total prevalence of haemosporidian infection by morphological and molecular examination was 59% and 73.9%, respectively. Binary logistic regression was carried out. The most prevalent infection was by Leucocytozoon spp. Most of the samples had mixed infections. The isolated genetic lineages of Leucocytozoon spp. were BUBT2, BUBT3, MILVUS01, ACNI1, BUBO01 and MILANS04. The detected genetic lineages of Plasmodium spp. were TURDUS1, BT7 and DONANA02. A new genetic lineage, BUTBUT17, was also identified.