In humans, like other mammals, females have two X chromosomes and males have one X and one Y chromosome. The Y chromosome contains a sex-determining gene SRY that kick-starts male development in the embryo and activates other genes that regulate the testicular development. Researchers have found that the Y chromosome seems to be disappearing, as seen in many other mammals, including rodents. The male eastern Europe vole and the spiny rats of Japan have completely lost their Y chromosomes and the Sry gene. However, the SOX9 protein plays a key role there in determining their sex. The new finding so support the possibility that humans too, may evolve a new sex determining mechanism. The sex chromosome genes act within cells to cause differences in phenotypes of XX and XY cells throughout the body. In the gonad, they determine the type of gonad, leading to differences in secretion of testicular vs. ovarian hormones, which cause further sex differences in tissue function. The human brains, as shown by neuroimaging, demonstrate variation in different areas of the brain that are associated with both differences in gonadal hormones, and in the number of X and Y chromosomes. In humans, males and females are different because of innate biological differences, and also they have different social and physical environments. Biologists tend to emphasize the importance of biological variables, and sociologists tend to emphasize the role of gendered environments. The Sry and the other Y-linked genes not only determine the differences in gonad development, they are also linked to maintaining gender balance (biologically) and various functions in the brain, including appropriate social responses by supporting behavioral flexibility, attention and emotion. In this article, we have reviewed the function of the Y chromosome and the Sry gene and their possible alternatives in case of their future extinction.