The aim of this study was to investigate the possible influence of estrogen receptor alpha (ERalpha) polymorphism on the craniofacial skeleton in female patients suffering from symptomatic osteoarthritis (OA) of the temporomandibular joint (TMJ). The sample comprised 76 genetically unrelated Korean women diagnosed with OA by research diagnostic criteria for temporomandibular disorders (RDC-TMD). Direct haplotyping procedure was used to analyze the PvuII and XbaI RFLPs. Twelve cephalometric measurements were taken to evaluate the spatial position and dimensions of the mandible. Mann-Whitney's U-test was used to identify the potential differences in the cephalometric measurements between the subjects grouped according to their carrier status for Px haplotype. In addition, an association study was carried out using chi(2)-test to further examine the relationship between Px haplotype and the craniofacial morphology of the symptomatic OA patients. Female symptomatic TMJ OA patients carrying Px haplotype showed significantly smaller facial axis angle (P<0.05) and mandibular body length (P<0.05) than the non-carriers. The association between the presence of Px haplotype and short mandibular body length was also ascertained. This study suggests that ERa polymorphism contributes to the altered mandibular dimensions in female symptomatic TMJ OA patients. Further studies on the role of the genetic markers relevant to the craniofacial growth and adaptation are expected to broaden our understanding of determinants of the craniofacial morphology.