Thalidomide is a teratogenic/hypnotic/sedative agent which elicits a wide range of pharmaceutical/biological activities. The diversity of its biological activities suggested that the drug might be useful as a multi-template for development of various kinds of biologically active compounds. We adopted two strategies for the structural development of thalidomide. The first was to develop the structure of the drug based on the target molecules to which thalidomide itself and/or its metabolites directly bind, or the assay systems in which thalidomide itself and/or its metabolites exhibit activity. Based on this strategy, tumor necrosis factor-alpha production-regulating agents, cyclooxygenase inhibitors, nitric oxide synthase inhibitors, histone deacetylase inhibitors, anti-angiogenic agents, and tubulin polymerization inhibitors have been created. The second was to develop the structure of thalidomide based on hypothetical target molecule(s)/biological response(s) which might be relevant to the pharmacological effects elicited by thalidomide. Based on this strategy, androgen antagonists, progesterone antagonists, cell differentiation inducers, aminopeptidase inhibitors, thymidine phosphorylase inhibitors, mu-calpain inhibitors, alpha-glucosidase inhibitors and nuclear liver X receptors (LXRs) antagonists have been created. Our structural development studies on thalidomide are reviewed focusing on recent development of tubulin polymerization inhibitors, alpha-glucosidase inhibitors, and nuclear liver X receptors antagonists.