Quantitative bone ultrasound (QUS) has a significant heritable component. Because estrogen is required for attainment of peak bone mass, we studied alleles of two genes, estrogen receptor α (ER1) and amplified in breast cancer-1 (AIB1), for their association with QUS. In a volunteer sample of 663 white women aged 18–35 years, bone ultrasound attenuation (BUA), speed of sound (SOS), and heel stiffness index (SI), the latter consisting of the component measures of BUA and SOS, were measured at the right calcaneus by QUS. Subjects were genotyped for the ER1 polymorphisms Xba I and Pvu II and for the AIB1 polyglutamine tract polymorphism. In a multiple regression analysis, ER1 genotype was an independent predictor of QUS-SI (p = 0.03). Because AIB1 and ER1 enhance gene expression in a coordinate manner, we also searched for interactions. A gene-by-gene interaction effect was seen for QUS-SI (p = 0.009), QUS-BUA (p = 0.03), and QUS-SOS (p = 0.004). These remained significant after the inclusion of clinically relevant variables into the final regression model. Overall, these clinical and genetic factors accounted for up to 16% of the variance in peak QUS; the genetic markers alone accounted for 4–7%. This is the first demonstration of specific genetic effects on calcaneal QUS encoded by alleles of genes directly involved in mediating estrogen effects on bone.