The socioeconomic structure of an early medieval society from the Mikulčice settlement (Czech Republic) was studied on the basis of an evaluation of the fluctuating and directional asymmetry (DA) of skulls. Two distinct inhabited regions, castle and sub-castle, were compared. Fluctuating asymmetry (FA) was used as a bioindicator of environmental stress, which is thought to have been different in the Mikulčice castle and sub-castle regions. DA is consistent with biomechanical loading, and it was expected to reflect different subsistence patterns. The material consisted of 129 crania from what was presumed to be a higher socioeconomic class (Mikulčice castle) and 71 crania from middle and lower socioeconomic classes (Mikulčice sub-castle). As a comparative sample, 138 crania from modern, lower socioeconomic classes (Pachner Collection) were used. The three-dimensional coordinates of 68 landmarks were digitized and analyzed using geometric morphometrics. In terms of DA, the highest values were recorded in the sub-castle sample and confirmed their lower socioeconomic position, with a grittier and lower protein diet compared with the castle sample. In terms of FA, distinctive differences between the sexes were found. In males, no differences were observed between castle and sub-castle, and the lowest FA values were recorded. In females, significantly higher values of FA were found, surprisingly in the castle sample, comparable with the more stressed Pachner Collection. We suspect that the FA reflects a more varied population of castle females as a consequence of patrilocality, although environmental stress remains a possibility. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.