The overexpression and/or mutation of the epidermal growth factor receptor family of tyrosine kinases, namely EGFR and HER-2, have been implicated in poor prognosis of human solid tumors and are under investigation as molecular targets for cancer therapy. To gain insights into selectivity in the interaction of inhibitors at the ATP site of the two kinases, we have carried out docking, comparative molecular field analysis (CoMFA), and comparative molecular similarity analysis (CoMSIA) 3D-QSAR studies on 50 benzylidene malonitrile derivatives. Docking studies indicate different binding modes (A, B, C, D, and E) that are dependent on the R(1) substituent of the compounds. Binding modes A and B are favored by compounds having a hydroxyl substituent at R(1) whereas a methoxy substituent at R(1) results in compounds occupying binding modes, C, D, and E. The compounds preferred modes A, B, and C in the apo-enzyme whereas modes B, D, and E were preferred in the enzyme in complex with erlotinib. For 3D QSAR studies, based on the multiple binding modes obtained from the docking, four composite alignment strategies (I, II, III, IV) were employed and compared with alignment V, which is based on pairwise atom alignment of the common structural elements. Alignments I and II produced models with better predictive ability than those from alignments III and IV against an external test set. In the EGFR kinase results, alignments I and II produced comparable 3D-QSAR models with alignment II being slightly better than I, whereas in the HER-2 results, alignment I was better than alignment II in its predictive ability. It appears that differences in binding mode preferences at the ATP site might constitute a reason for the selectivity of the dihydroxy compounds as inhibitors of EGFR relative to HER-2. They are more likely to have multiple binding modes at the ATP site of EGFR, i.e., either modes A or B, than in the ATP site of HER-2 where they are possibly limited to only binding mode, A. Selectivity of the methoxy compounds on the other hand appears to depend on hydrogen bonding interactions involving the cyano group and residue 751 in the ATP site.