The histological basis of the human uterine endometrium has been established by 2D observation. However, the fundamental morphology of endometrial glands is not sufficiently understood because these glands have complicated winding and branching patterns. To construct a big picture of endometrial gland structure, we performed tissue-clearing-based 3D imaging of human uterine endometrial tissue. Our 3D immunohistochemistry and 3D layer analyses revealed that endometrial glands formed a plexus network in the stratum basalis, similar to the rhizome of grass. We then extended our method to assess the 3D morphology of adenomyosis, a representative "endometrium-related disease", and observed 3D morphological features including direct invasion of endometrial glands into the myometrium and an ant colony-like network of ectopic endometrial glands within the myometrium. Thus, 3D analysis of the human endometrium and endometrium-related diseases will be a promising approach to better understand the pathologic physiology of the human endometrium. lives of women from puberty until after menopause (Garcia-Solares et al., 2018;Koninckx et al., 2019;Morice et al., 2016). However, the pathogenesis of endometrium-related diseases remains unclear, and further investigations focusing on the endometrium from the standpoint of disease prevention are required.The conventional morphological theory of endometrial structure has been established based on two-dimensional (2D) histological observation (Johannisson et al., 1982;McLennan and Rydell, 1965;Noyes et al., 1950). Histologically, the endometrium is lined by a simple luminal epithelium and contains tubular glands that radiate through endometrial stroma toward the myometrium via coiling and branching morphogenesis (Gray et al., 2001). The human endometrium is stratified into two zones:the stratum functionalis and the stratum basalis. The stratum functionalis is shed during menstruation and regenerates from an underlying basal layer during the proliferative period. Therefore, it is widely assumed that regeneration of the stratum functionalis depends on endometrial progenitor/stem cells residing in the stratum basalis (Kyo et al., 2011;Maruyama and Yoshimura, 2012;Padykula, 1991;Prianishnikov, 1978). Despite this well-established understanding, neither the detailed mechanisms of endometrial regeneration during the menstrual cycle nor the localization of endometrial progenitor/stem cells have been fully characterized (Garry et al., 2010;Gellersen and Brosens, 2014;Santamaria et al., 2018). One of the reasons for this knowledge gap is that the fundamental structure of the human endometrium has not been sufficiently clarified. Since human endometrial glands have complicated winding and branching morphologies, it is extremely difficult to assess the whole shapes of glands by only 2D histopathology imaging.In our previous genomic study, sequence analysis of 109 single endometrial glands revealed that each gland carried distinct somatic mutations in cancer-associated genes such as PIK3CA, KRAS...