Hedgehog is a morphogen essential for body patterning and proper embryonic development from flies to humans. Thought quiescent in adults, its inappropriate reactivation is associated with many disparate genetic and sporadic types of human cancers. Recent findings have demonstrated a key, yet unexpected, role of the Hedgehog signaling pathway in metabolic control. Here, we describe a panel of methods to determine and analyze cellular and organismal metabolic changes downstream of the Hedgehog signaling pathway.