A newly developed descriptor, three- dimensional holographic vector of atomic interaction field (3D-HoVAIF), was used to describe the chemical structures of purine bases. After variable screening by stepwise multiple regression (SMR) technique, a partial least square (PLS) regression model was built with 3D-HoVAIF. The model was satisfactory com- paring to reference since correlation coefficients of molecular modeling ( Rc 2um), cross- validation ( Qc 2um) and standard deviation of estimation (SD) were 0.966, 0.860 and 0.112, respectively, showing that the model had favorable estimation and prediction capa- bilities. It was illustrated that information related to retention data of purine bases could preferably be expressed by 3D-HoVAIF with definite physico- chemical meanings and easy structural interpretation for purine bases. It was illustrated that 3D-HoVAIF was to preferably express retention data of purine bases and had definite physicochemical significance. So 3D-HoVAIF was a useful structural expression technique for quantitative structure activity (or prop- erty or retention) relationships (QSAR/QSPR/QSRR) study, such as structural characterization and chro- matographic retention prediction. A newly developed descriptor, three-dimensional holographic vector of atomic interaction field (3D-HoVAIF), was used to describe the chemical structures of purine bases. After variable screening by stepwise multiple regression (SMR) technique, a partial least square (PLS) regression model was built with 3D-HoVAIF. The model was satisfactory com- paring to reference since correlation coefficients of molecular modeling (Rc 2um), cross- validation (Qc 2um) and standard deviation of estimation (SD) were 0.966, 0.860 and 0.112 , respectively, showing that the model had favorable estimation and prediction capa- bilities. It was illustrated that information related to retention data of purine bases could preferably be expressed by 3D-HoVAIF with definite physico-chemical meanings and easy structural interpretation for purine bases. It was illustrated that 3D-HoVAIF was to express retention data of purine bases and had definite physicochemical significance. So 3D-HoVAIF was a use ful structural expression technique for quantitative structure activity (or proprty or retention) relationships (QSAR / QSPR / QSRR) study, such as structural characterization and chro-matographic retention prediction.