3D-QSAR and molecular docking analysis were performed to explore the interaction of estrogen receptors (ERalpha and ERbeta) with a series of 3-arylquinazolinethione derivatives. Using the conformations of these compounds revealed by molecular docking, CoMFA analysis resulted in the first quantitative structure-activity relationship (QSAR) and first quantitative structure-selectivity relationship (QSSR) models predicting the inhibitory activity against ERbeta and the selectivity against ERá. The q(2) and R(2) values, along with further testing, indicate that the obtained 3D-QSAR and 3D-QSSR models will be valuable in predicting both the inhibitory activity and selectivity of 3-arylquinazolinethione derivatives for these protein targets. A set of 3D contour plots drawn based on the 3D-QSAR and 3D-QSSR models reveal modifications of substituents at C2 and C5 of the quinazoline which my be useful to improve both the activity and selectivity of ERbeta/ ERalpha. Results showed that both the steric and electrostatic factors should appropriately be taken into account in future rational design and development of more active and more selective ERbeta inhibitors for the therapeutic treatment of osteoporosis.