This study examines regional differences in the gender wage gap in Spain using matched employer-employee microdata, two different econometric decomposition methods and panel data techniques. Our findings suggest that Spain shows a significant regional heterogeneity in the size of the raw gap, roughly comparable to cross-country differences observed in the European context. The results from the decomposition analysis show that although the bulk of the gender wage gap in Spanish regions is due to differences in the endowments of productive characteristics between males and females there is still a substantial part of the gap that remains unexplained. The analysis of the causes behind the variation of both, the raw and the unexplained gender wage gap by region highlights that several economic, institutional and demographic elements identified in previous studies analysing international differences in the gender wage gap are also relevant to explain regional differences in the gender wage gap in Spain.