Developmental instability (DI), as measured by fluctuating asymmetry (FA), may reflect fitness and facilitate the expression of morphological variation. Insights in the underlying mechanisms and magnitude of DI during early development would increase our understanding of its role in evolutionary biology. We studied associations between FA and congenital abnormalities of different origins and functional systems in deceased human fetuses. Major congenital abnormalities corresponded to severe, often-lethal developmental disorders disrupting normal development from early organogenesis onward, but only moderately increased FA. Lower FA with age also supported the hypothesis that more severe abnormalities, leading to an earlier death, increased DI. Although FA related significantly to measures of fitness or health, we anticipated stronger associations because fetal health problems were detrimental. Furthermore, elevated FA occurred in only 4 of 17 disorders (left—right patterning, limb defects, and problems of bronchopulmonary and urogenital system). Fetuses experiencing major abnormalities other than these four types did not show increased FA. This suggests that the functional importance of symmetry in limbs has resulted in strong selection for symmetry and reduced its sensitivity to stress. Finally, the observed patterns suggest that specific developmental pathways have a stronger effect on DI than others do.