Endogenous substances are those that originate from within an organism, tissue, or cell.

Endogenous viral elements (EVEs) 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 processes include senescence, the menstrual cycle and the self-sustained circadian rhythms of plants and animals.

In some biological systems, endogeneity refers to the recipient of DNA (usually in prokaryotes). However, because of homeostasis, discerning between internal and external influences is often difficult.

Endogenous transcription factors refers to those that are manufactured by the cell, as opposed to cloned transcription factors.