Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm was used to study the correlation between the physicochemical properties and the in vitro bioactivities of ginkgolide analogues. The correlation derived from CoMFA analysis has a good predictive capability. Based on the result of CoMFA analysis, we designed some compounds. Pharmacological assay indicated that three of these new designed compounds are 2 and 4 times more potent than that of ginkgolides.