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Background: Biotransformed bufadienolides are new kind of cytotoxic products with novel structures. Method: Herein, 3D-QSAR analyses were performed on bufadienolides using CoMFA and CoMSIA to learn the structure-activity relationship and the mechanism of action of these compounds. The cross-validated q2value of CoMFA is 0.648 and q2value of CoMSIA is 0.635. The non-crossvalidated r2 value of CoMFA is 0.963 and r2 values of CoMSIA is 0.961. The 3D-QSAR models we obtained were illustrated through CoMFA and CoMSIA contour plots. Results: That will be valuable in predicting cytotoxic activities against cancer cells, and could be used to design potent anticancer drugs.