The electron conformational genetic algorithm (EC-GA) method has been employed as a 4D-QSAR approach to reveal the pharmacophore (Pha) and to predict anticancer activity in the N-morpholino triaminotriazine derivatives. The electron conformational matrices of congruity (ECMCs) identified by electronic and structural parameters are constructed from data of conformational analysis and electronic structure calculation of molecules. Comparing the matrices, electron conformational submatrix of activity (ECSA, Pha) are revealed that are common for these compounds within a minimum tolerance. To predict the theoretical activity of training and test set and to select important variables for describing the activities, genetic algorithm and non-linear least square regression methods were applied. Regression coefficients were found 0.9708 for training and 0.9520 for test set. (C) 2010 Elsevier Masson SAS. All rights reserved.