Hypoxanthine is widely used in biochemical research as a precursor for the synthesis of nucleotides, particularly in studies involving DNA and RNA metabolism. It plays a crucial role in cell culture media, where it serves as a supplement to support the growth of certain cell lines, especially those requiring purine salvage pathways.

In medical diagnostics, hypoxanthine is a biomarker for assessing tissue hypoxia and ischemia, as its levels increase under oxygen-deficient conditions. Additionally, it is utilized in the production of pharmaceuticals, including drugs that target gout and other metabolic disorders, by influencing purine metabolism.

In the food industry, hypoxanthine is monitored as an indicator of freshness in seafood, as its accumulation correlates with spoilage. Its applications also extend to enzymology, where it acts as a substrate for enzymes like xanthine oxidase, aiding in the study of enzymatic reactions and inhibitor development.