Uroplakin (Upk) 3 is one of the main structural components of the urothelium tissue. Although expression of UPK3B is seen in a wider variety of the tissues and organs than UPK3A, tissue-specific expression has not yet been analyzed. Here, we analyzed the Cre recombinase activity driven by the Upk3b promoter in transgenic mice and the endogenous localization of UPK3B. We generated Tg(Upk3b-Cre)/R26tdTomato mice by crossing ROSA26tm14(CAG-tdTomato) (R26tdTomato) mice with Tg(Upk3b-Cre) mice and investigated the spatiotemporal distribution of tdTomato in embryonic and adult mice. In embryos, we detected Cre recombinase activity in neural crest cells and the heart, liver, kidneys, and lungs. In adult mice, Cre recombinase activity was detected in male and female genital organs; however, the activity was absent in the bladder. Histological analyses revealed that both tdTomato and UPK3B were present in testicular and epididymal sperm; however, tdTomato was not present in the ductus epididymis, where the endogenous expression of UPK3B was detected. In female siblings, both tdTomato and UPK3B expressions were detected in the follicles of the ovary, whereas no tdTomato expression was found in the mucosal epithelium of the fallopian tubes, where the endogenous UPK3B was expressed. These data suggest that UPK3B may play a pivotal role in the maturation of gametes and gamete-delivery organs.