Pleiotropy is the phenomenon where one gene has multiple different phenotypes associated with it. For instance, the gene may code for a product that is used in many cells, or for a signalling molecule that has a widespread endocrine effect.

An example of a pleiotropic gene is one in mice responsible for coat colour. The dominant allele for this gene is Y, for yellow coat colour, and the recessive is y, for agouti coat colour. The genotype yy gives agouti mice and the genotype Yy gives yellow mice. However, the genotype YY never surfaces phenotypically because the Y allele, when available in two copies, also causes lethality (premature termination of the embryo). Thus, Y has a pleiotropic effect: coat colour and lethality.

Pleiotropy can be problematic when selection favours one allele of the gene for one trait, and the other allele of that gene for another trait. Antagonistic pleiotropy refers to a gene that has a mixture of beneficial and detrimental phenotypic effects. This idea is related to the theory of ageing: that increased fitness in youth (for reproduction) causes decreased fitness in old age. For instance, a gene codes for the protein p53 which suppresses cell proliferation and thereby prevents cancer. However, it also prevents stem cell proliferation, hence the inability to replenish worn-out tissues later in life.

Pleiotropy is distinct from polygenic traits, where one phenotype is associated with multiple different genes.