Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of its nucleoside inosine. It has a tautomer known as 6-hydroxypurine. Hypoxanthine is a necessary additive in certain cells, bacteria, and parasite cultures as a substrate and nitrogen source. For example, it is commonly a required reagent in malaria parasite cultures, since Plasmodium falciparum requires a source of hypoxanthine for nucleic acid synthesis and energy metabolism.

In August 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting hypoxanthine and related organic molecules, including the DNA and RNA components adenine and guanine, may have been formed extraterrestrially in outer space.

The Pheretima aspergillum worm, used in Chinese medicine preparations, contains hypoxanthine.