Insulin-like growth factor?1 receptor (IGF-1R) has proven as a key oncology target. Recently derivatives of 1,3-disubstituted-imidazo[1,5-] pyrazine have been found as potent IGF-IR inhibitors. Three dimensional quantitative structure activity relationship (3D-QSAR) studies have been performed for this series of compounds and validity of 3D-QSAR models compared for two major alignment schemes, namely ligand-based and receptor-guided alignment schemes. As a result, receptor guided alignment schemes yielded better 3D-QSAR models for both comparative molecular field analysis (CoMFA) (q2=0.53, r2=0.95) and comparative molecular similarity indices analysis (CoMSIA) (q2=0.51, r2=0.86). This might arise from the more accurate inhibitor alignment using structural information of the active site. Therefore the receptor-guided 3D-QSAR may be helpful to design more potent IGF-1R inhibitors as well as to understand the inhibitor binding.