Symptoms of virus and viroid infections have been observed during the last ten years in stone fruit crops, however, no relative incidences of virus and viroid diseases have been reported on stone fruit crops in western Anatolia, Turkey. Large-scale surveys were conducted from June to August between the years 2004 and 2006 in the main stone fruit growing orchards and mother blocks of western Anatolia to determine the seven most important virus and two important viroid affecting Prunus species. The results of serological (ELISA) and molecular (PCR and tissue-printing molecular hybridization) tests demonstrated the occurrence of Plum pox virus (PPV), Prune dwarf virus (PDV), Prunus necrotic ringspot virus (PNRSV), Apple chlorotic leaf spot virus (ACLSV), Apple mosaic virus (ApMV), Apricot latent virus (ApLV), Plum bark necrosis stem pitting-associated virus (PBNSPaV), Peach latent mosaic viroid (PLMVd), and Hop stunt viroid (HSVd) in tested 1732 specimens of stone fruits. The overall infection level with these graft-transmissible agents was 30%. The results showed that PDV is predominant in stone fruit crops. To our knowledge, PBNSPaV was reported for the first time in western Anatolia. The results obtained in this study illustrate a need for certification or clean stock program to prevent the occurrence and the spread of graft transmissible agents in western Anatolia.