The aim of this study was to investigate the geographical variation of diabetes prevalence in Greece. The database of Diabetes Mellitus Patients Registry of the National Organization for Health Care Services Provision, was used to identify patients of type 1 and type 2 diabetes. Incidence rates were estimated by type of diabetes and sex for each prefecture of Greece and spatial analysis was performed to recognize statistically significant spatial clusters across the country. 424,118 patients of type 1 and type 2 diabetes had been registered in the Diabetes Mellitus Patients Registry. Type 1 diabetes prevalence was 0.24% and type 2 was 3.66%. Mapping diabetes prevalence revealed the highest rates of type 1 in the Greek islands, whereas the highest rates of type 2 diabetes were identified in northern and eastern prefectures of Greece. Spatial clusters of high values of diabetics were noticed in northwest and northeast Greece, for type 1 and type 2 diabetes respectively. In type 1, men patients prevailed to women in most Greek prefectures, while type 2 men to women ratio highlighted the female predominance in north, central and east Greece. The present study underlines geospatial surveillance as a useful tool by more precisely determining the underlying spatial epidemiology of diabetes.