Blastocystis is an anaerobic parasitic microorganism which has been found in the intestinal tract of many vertebrates including humans and dogs. Recently, members of Blastocystis sp. were classified into nine sub-types, based on phylogenetic trees derived from sequence analysis of the small sub-unit ribosomal RNA gene. The pathogenesis of Blastocystis in the dog remains uncertain and the existence of pathogenic and non-pathogenic sub-types is under investigation. Feacal samples from 30 privately owned and 42 stray dogs, originated from central and northern Greece, were examined by both light microscopy and PCR assays for the detection of Blastocystis sp. All samples were found to be negative by both assays. It seems that, in Greece, the dog is unlikely to be a “reservoir” of Blastocystis sp., although a large scale epidemiologic study is needed to be carried out in order for more conclusive results to be drawn.