Structured Abstract Objectives Asymmetry has been noted in the human craniofacial region in several pathological conditional and growth abnormalities, often with a directional predilection. Physiological asymmetry has also been reported in normal adults and adolescents, with certain regions of the cranioskeleton, such as the mandible, displaying prevalent asymmetry. However, the timing at which such asymmetries arise has not been evaluated. The objectives of this study were to assess the degree of asymmetry in facial bones during the foetal stages of human development. Material and Methods Twenty‐one preserved conceptuses from the Congenital Anomaly Research Center at Kyoto University, between ages 15 and 20 weeks of gestation, were studied using high‐resolution μCT imaging. Asymmetry analysis was performed on digitally segmented facial bone pairs, using geometric morphometric (GM) approaches as well as adapted deformation‐based asymmetry (DBA) methods. Results GM analysis revealed that the developing facial bones display statistically significant fluctuating and directional asymmetry. DBA methods suggest that the magnitude of asymmetry in facial bones is low and does not appear to be correlated to the estimate of overall size of conceptus. Additionally, the patterns of asymmetry are highly variable between individual specimens. Conclusions The developing foetal facial skeleton displays variable patterns of low magnitude asymmetry. GM and DBA methods offer unique advantages to assess facial asymmetry quantitatively and qualitatively.