A tooth germ ex vivo organ culture allows visualization of its development in different stages, thus enabling investigation of the molecular mechanisms of regulatory factors. Tooth germs can be rapidly dissected from E13 mouse embryos and placed on cell culture inserts for observation of subsequent tooth germ development in a three-dimensional situation in real time. This method is also suitable for other organs that develop by epithelial-mesenchymal interactions, including salivary gland, hair, lung, and kidney. In addition, siRNAs or growth factors can be easily added to ex vivo tooth germ cultures to investigate the detailed molecular function of specific genes. The present protocol provides an efficient and practical method for isolation and ex vivo culture of embryonic tooth germs.