Explanations for the emergence and abandonment of the Chalcolithic Trypillia mega-sites have long been debated. Here, the authors use Gini coefficients based on the sizes of approximately 7000 houses at 38 Trypillia sites to assess inequality between households as a factor in the rise and/or demise of these settlements. The results indicate temporarily reduced social inequality at mega-sites. It was only after several generations that increased social differentiation re-emerged and this may explain the subsequent abandonment of the mega-sites. The results indicate that increases in social complexity need not be associated with greater social stratification and that large aggregations of population can, for a time at least, find mechanisms to reduce inequality.