Children exposed prenatally to antiepileptic drugs may have a typical facies characterized by midfacial retrusion, a short nose, and anterverted nares. We sought to examine these effects in more detail by using geometric morphometrics (GM). The lateral cephalograms of 65 children exposed prenatally to monotherapy (phenobarbital, phenytoin, or carbamazepine) were analyzed using principal component analysis (PCA) and discriminant function analysis (DFA), and the resulting configurations compared with those of control children. PCA revealed significant separation between the means when PC1 was plotted against PC 2 for all the areas studied: maxilla, entire cranial base, spheno-occipital region, and the total study area. DFA showed a shorter maxilla but taller sphenoidal body, nasion and orbitale more inferior, anterior nasal spine more superior, and sella turcica projected posteriorly and upward. Cross-validation accurately classified between 79.5% − 88.6% of the control group and between 73.8% and 81.5% of the study group when looking at the three anatomic regions. These details may help isolate the mechanism for the anomalies because of GM’s use of shape instead of traditional linear and angular cephalometric measurements.