The Y chromosome is one of the two sex-determining chromosomes in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development if present. The human Y chromosome is composed of about 50 million base pairs. DNA in the Y chromosome is passed from father to son, and Y-DNA analysis may thus be used in genealogy research. With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest evolving parts of the human genome.

Most mammals have only one pair of sex chromosomes in each cell. Males have one Y chromosome and one X chromosome, while females have two X chromosomes. In mammals, the Y chromosome contains a gene, SRY, which triggers embryonic development as a male. The Y chromosomes of humans and other mammals also contain other genes needed for normal sperm production.

There are exceptions, however. For example, the platypus relies on an XY sex-determination system based on five pairs of chromosomes. Platypus sex chromosomes in fact appear to bear a much stronger homology (similarity) with the avian Z chromosome, and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination. Among humans, some men have two Xs and a Y ("XXY", see Klinefelter's syndrome), or one X and two Ys (see XYY syndrome), and some women have three Xs or a single X instead of a double X ("X0", see Turner syndrome). There are other exceptions in which SRY is damaged (leading to an XY female), or copied to the X (leading to an XX male). For related phenomena see Androgen insensitivity syndrome and Intersex.