1,25-Dihydroxyvitamin D_3, an active form of vitamin D_3, which plays a central role in the regulation of calcium and bone homeostasis through vitamin D receptor (VDR). In 1994, Morrison and colleagues first reported that bone mineral density was associated with single nucleotide polymorphisms (SNPs) in the intron 8 of human VDR gene. In 1997, we clarified the whole structure of the human VDR genome and reported the relationship between FokI and Cdx-2 SNPs in the human VDR gene and bone density in Japanese women. Osteoporosis is known as one of multifactorial genetic diseases and its occurrence is associated with not only genetic factors but also environmental factors, lifestyle such as diet and exercise, aging, and abnormal bone mineral metabolism. Therefore, it can be expected that the identification of osteoporosis-related genes including the VDR gene will lead to the development of new methods to treat and to protect against osteoporosis, although there are several statistical problems for data analysis.