It is one of the products of the action of xanthine oxidase on xanthine. However, more frequently in purine degradation, xanthine is formed from oxidation of hypoxanthine by xanthine oxidoreductase.Hypoxanthine-guanine phosphoribosyltransferase converts hypoxanthine into IMP in nucleotide salvage.Hypoxanthine is also a spontaneous deamination product of adenine. Because of its resemblance to guanine, the spontaneous deamination of adenine can lead to an error in DNA transcription/replication, as it binds with cytosine.

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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 cell, 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.