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This paper examines the degree of synchronicity in business cycles in Greek regions associated with specific spatial and economic characteristics that explain, to a large extent, synchronisation dynamics. We conducted an analysis of almost 30 years’ (1980-2008) worth of data at the NUTSIII level (prefectures). We conclude that prefectures are more synchronised with the NUTSII regions than the national level, accentuating a regional (NUTSII) border effect. Moreover, the intensification of the integration process and the free operation of markets seem to diachronically affect the structural characteristics of the Greek regions and the geography of cyclical synchronisation. Our study revealed a two-stage integration in which in the first stage they are detected urbanisation economies, while in the second one localisation economies. The metropolitan region, apart from its prominent position in economic growth, shows a confined level of business synchronisation with the other regions, stressing Greece’s pattern of economic and structural dualism.