Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a set of pyridinone derivatives. A molecular alignment obtained by docking of compounds into the non-nucleoside reverse transcriptase inhibitor binding site of HIV-1 was used. Good correlations between the calculated binding free energies and experimental inhibitory activities suggest that the binding conformations of these inhibitors are reasonable. Robust and predictive 3D-QSAR models were obtained with q2 values of 0.706 and 0.723 for CoMFA and CoMSIA, respectively. The models were validated by an external test set obtaining r2 pred values of 0.720 and 0.750 for CoMFA and CoMSIA, respectively. The CoMFA, CoMSIA and docking results help to understand the type of interactions that occur between pyridinone derivatives with the non-nucleoside reverse transcriptase inhibitor binding pocket, and explain the viral resistance to pyridinone derivatives upon mutation of amino acids Tyr181 and Tyr188. The results obtained provide information for a better understanding of the drug resistant mechanisms. The 3D-QSAR models derived will be used to guide the design of pyridinone derivatives active against mutant strains of reverse transcriptase.