Glycogen synthase kinase 3 (GSK-3) is a serine/threonine kinase that has captured great attention in drug discovery projects. Structure based design has been successfully carried out to find a novel class of GSK-3 inhibitors using the Ludi de novo ligand design program. A total of 15 potential leads are suggested from the study. The structures have been validated through detailed analysis of the Ludi score values and by molecular docking experiment using FlexX. The hits have been further verified through: (1) visual examination of how well the hits dock into the GSK-3beta binding site; (2) comparative analysis of their FlexX, G_Score, PMF_Score, ChemScore, and D_scores values; (3) a comparative investigation of the docking scores of the hits with those of the reported inhibitors after calibration of the docking procedure with 17 previously reported inhibitors; (4) determination of the binding mode of the hits and comparison with that of the so far known inhibitors. Hits retaining interactions with the common amino acids of GSK-3beta binding site were taken to represent potential leads. Structurally the hits designed are mainly flat nitrogen heterocycles. These hits are expected to be important additions to the search of GSK-3 inhibitors and may provide invaluable insights to further understand the structural basis of catalysis and inhibition of this kinase.