Pseudoautosomal regions (PARs) on the Y chromosome share homology with regions on the X chromosome and synapse with it during spermatogenesis to allow segregation of the sex chromosomes.

Most of the Y chromosome is a "male-specific" (MSY) area composed of euchromatic regions containing functional genes and heterochromatic regions lacking genes.

One gene in the euchromatic region is the "sex-determining region" (SRY) which encodes a testis-determining factor (TDF) that triggers differentiation of testes tissue in the embryo.