In the late 1980s, Peter Goodfellow in London, UK led a team of researchers who showed that the SRY gene in humans codes a protein that causes testes to develop in embryos. During this time, scientists in London and Paris, including Peter Koompan and John Gubbay, proposed that SRY was the gene on the Y chromosome responsible for encoding the testis-determining factor (TDF) protein. The TDF is a protein that initiates embryo to develop male characteristics. Looking for evidence that SRY was the TDF, Goodfellow and colleagues examined people who were anatomically female, but whose cells had Y chromosomes. Females normally have cells with two X sex chromosomes (XX), while males normally have cells with one X and one Y chromosome (XY). Goodfellow's team discovered that individuals with Y chromosomes developed as female instead of as male due to inactive SRY sequences on the Y chromosome. Goodfellow and colleagues compiled the results of their experiment in a paper titled Genetic Evidence Equating SRY and the Testis-Determining Factor in 1990. Their results showed that the SRY gene is necessary for male characteristics to develop in embryos, and that SRY encodes the TDF protein.

The Sex-determining Region Y (Sry in mammals but SRY in humans) is a gene found on Y chromosomes that leads to the development of male phenotypes, such as testes. The Sry gene, located on the short branch of the Y chromosome, initiates male embryonic development in the XY sex determination system. The Sry gene follows the central dogma of molecular biology; the DNA encoding the gene is transcribed into messenger RNA, which then produces a single Sry protein. The Sry protein is also called the testis-determining factor (TDF), a protein that initiates male development in humans, placental mammals, and marsupials. The Sry protein is a transcription factor that can bind to regions of testis-specific DNA, bending specific DNA and activating or enhancing its abilities to promote testis formation, marking the first step towards male, rather than female, development in the embryo.

Early 1990s research conducted by Peter Koopman, John Gubbay, Nigel Vivian, Peter Goodfellow, and Robin Lovell-Badge, showed that chromosomally female (XX) mice embryos can develop as male with the addition of a genetic fragment from the Y chromosome of male mice. The genetic fragment contained a segment of the mouse Sry gene, which is analogous to the human SRY gene. The researchers sought to identify Sry gene as the gene that produced the testis determining factor protein (Tdf protein in mice or TDF protein in humans), which initiates the formation of testis. Koopman's team published their results in 1991 in Male Development of Chromosomally Female Mice Transgenic for Sry gene. Their results showed that Sry gene partly determines the sex of an embryo and is the only gene on the Y chromosome necessary for initiation of male development in mice.

Theophilus Shickel Painter studied the structure and function of chromosomes in the US during in the early to mid-twentieth century. Painter worked at the University of Texas at Austin in Austin, Texas. In the 1920s and 1930s, Painter studied the chromosomes of the salivary gland giant chromosomes of the fruit fly (Drosophila melanogaster), with Hermann J. Muller. Muller and Painter studied the ability of X-rays to cause changes in the chromosomes of fruit flies. Painter also studied chromosomes in mammals. He investigated the development of the male gamete, a process called spermatogenesis, in several invertebrates and vertebrates, including mammals. In addition, Painter studied the role the Y-chromosome plays in the determination and development of the male embryo. Painter's research concluded that egg cells fertilized by sperm cell bearing an X-chromosome resulted in a female embryo, whereas egg cells fertilized by a sperm cell carrying a Y-chromosome resulted in a male embryo. Painter's work with chromosomes helped other researchers determine that X- and Y-chromosomes are responsible for sex determination.

The Y-chromosome is one of a pair of chromosomes that determine the genetic sex of individuals in mammals, some insects, and some plants. In the nineteenth and twentieth centuries, the development of new microscopic and molecular techniques, including DNA sequencing, enabled scientists to confirm the hypothesis that chromosomes determine the sex of developing organisms. In an adult organism, the genes on the Y-chromosome help produce the male gamete, the sperm cell. Beginning in the 1980s, many studies of human populations used the Y-chromosome gene sequences to trace paternal lineages. In mammals, the Y-chromosomes contain the master-switch gene for sex determination, called the sex-determining region Y, or the SRY gene in humans. In most normal cases, if a fertilized egg cell, called a zygote, has the SRY gene, the zygote develops into an embryos that has male sex traits. If the zygote lacks the SRY gene or if the SRY gene is defective, the zygote develops into an embryo that has female sex traits.

Y-chromosomes exist in the body cells of many kinds of male animals. Found in the nucleus of most living animal cells, the X and Y-chromosomes are condensed structures made of DNA wrapped around proteins called histones. The individual histones bunch into groups that the coiled DNA wraps around called a nucleosome, which are roughly 10 nano-meters (nm) across. The histones bunch together to form a helical fiber (30 nm) that spins into a supercoil (200 nm). During much of a cell's life, DNA exists in the 200 nm supercoil phase.