The arrangement of cells within a tissue plays an essential role in organogenesis, including tooth development. Organ morphogenesis and physiological functions induced by three-dimensional tissue organization are well known to be regulated by the proper spatiotemporal organization of various signaling molecules, including cytokines, extracellular matrix proteins, and adhesion molecules. Development of a three-dimensional cell manipulation technology to create a bioengineered organ germ, designated as the organ germ method, enabled the generation of a structurally correct and fully functional bioengineered tooth in vivo. This method is expected to be utilized as a valuable technique for analyzing gene and protein functions during organogenesis. Here, we describe protocols for tooth germ reconstitution using the organ germ method and methods for analyzing tooth development in vitro and in vivo.