We are becoming increasingly aware of regional data patterning in the archaeological record of Prepalatial Crete, yet a theoretically informed and methodologically systematic study assessing the significance of such differences is still lacking. This article investigates variation through the rich mortuary record of the period and explores the significance of such diversity for our understanding of Prepalatial Crete. A detailed analysis using mortuary data reveals a complex spatial and temporal variation in the record which raises questions about social, political and ideological differences between communities on the island during the early periods of the Early Bronze Age. Prepalatial Crete emerges from this analysis as a complex context resulting from an intricate combination of local and regional histories and trajectories and far from the unified culture that the term ‘Minoan’ implies.