Pharmacophore mapping studies were undertaken for a set of 29 flavonoids as α-glucosidase inhibitors. Four point pharmacophores with two hydrogen bond acceptor, one hydrogen bond donor and one aromatic ring as pharmacophoric features were developed. Amongst them the pharmacophore hypothesis AADR1 yielded a statistically significant 3D-QSAR model with 0.903 as R2 value and was considered to be the best pharmacophore hypothesis. The developed pharmacophore model was externally validated by predicting the activity of test set molecules. The squared predictive correlation coefficient of 0.69 was observed between experimental and predicted activity values of test set molecules. The geometry and features of pharmacophore were expected to be useful for the design of selective α-glucosidase inhibitors.