Purmorphamine, a 2,6,9-trisubstituted purine compound, was identified as a potent osteogenic differentiation inducing molecule through a high throughput chemical screen in C3H10T1/2 cells. Expression profiling of cells treated with purmorphamine in conjunction with systematic pathway analysis was used to reveal that the Hedgehog/Hh signaling pathway is the primary affected biological network and purmorphamine is a selective Hh pathway agonist, which was further confirmed by chemical epistasis using two different Hh pathway antagonists: cyclopamine that binds and inhibits Smoothened (Smo), and forskolin that activates protein kinase A (PKA), which converts Gli proteins to transcriptional repressors by phosphorylation.