Endogenous substances and processes are those that originate from within a system such as an organism, tissue, or cell.^[2] The term is chiefly used in biology but also in other fields.^[1]

Endogenous substances and processes contrast with exogenous ones, such as drugs, which originate from outside of the organism.

Cell signalling systems such as hormone and neurotransmitter systems use endogenous substances. Endogenous substances can regulate sleep.^{[3] []} Examples of endogenous substances, and systems that use them, include

Endogenous transcription factors are those manufactured by the cell, as distinguished from cloned transcription factors.

Endogenous substances typically have some physiological utility. However substances can also be pathologically endogenous. For example, in auto-brewery syndrome, ethanol is endogenously produced within the digestive system through endogenous fermentation of sugars.

Endogeneity can, in some biological systems, particularly with viruses and prokaryotes, pertain to DNA incorporated (endogenized) into the organism.^[9] However, because of homeostasis, discerning between internal and external influences is often difficult. Endogenous viral elements, which are DNA sequences derived from viruses that are ancestrally inserted into the genomes of germ cells. These sequences, which may be fragments of viruses or entire viral genomes (proviruses), can persist in the germline, being passed on from one generation to the next as host alleles. Endogenous retroviruses are a type of endogenous viral element.

Endogenous effects can modulate and regulate systems, in conjunction with environmental influences.^{[10] []}

Endogeny can refer to changes that originate from within a system.^{[10] []} Endogenous changes can occur in social systems and can be modelled by Marxian dialectics.^{[10] []}

Orthogenesis is a similar concept to endogeny but refers to changes within separate systems that results in their evolution along similar paths.^{[10] []} The concept of orthogenesis has never been widely favored in evolutionary biology.^{[10] []}

Examples of endogenous processes include:

Endogenous processes can also be pathological. For example, endogenous depression is an atypical type of depression caused by internal effects, such as cognitive and biological stressors.

All processes that take place inside Earth (and other planets) are considered endogenous. They make the continents migrate, push the mountains up, and trigger earthquakes and volcanism. Endogenous processes are driven by the warmth that is produced in the core of Earth by radioactivity and gravity.

An emotion or behavior is endogenous if it is spontaneously generated from an individual's internal state.

A variable is called endogenous if it is explained within the model in which it appears. For example, in a supply and demand model of an agricultural market, the price and quantity of trade would be the endogenous variables explained by the model; changes in the weather or in consumer tastes would be exogenous variables that might shift the supply and demand curves.

In political science, something is endogenous if it is actually the result of the action for which it is generally labeled the cause. For example, ethnic violence is generally thought to be caused by ethnic division. However, endogeny would say that ethnic divisions are a result of ethnic violence.