In organogenesis including lacrimal gland development, cell arrangement within a tissue plays an important role. The lacrimal gland develops from embryonic ocular surface epithelium through reciprocal epithelial and mesenchymal interaction, which is organized by interactive regulation of various pathways of signaling molecules. Current development of an in vitro three-dimensional cell manipulation procedure to generate a bioengineered organ germ, named as the organ germ method, has shown the regeneration of a histologically correct and fully functional bioengineered lacrimal gland after engraftment in vivo. This method demonstrated a possibility of lacrimal gland organ replacement to treat dry eye disease, which has been a public health problem leading reduction of visual function. Here, we describe protocols for lacrimal gland germ regeneration using the organ germ method and methods for analyzing the function of the bioengineered lacrimal gland after its transplantation in vivo.