Autofluorophores are endogenous fluorescent compounds that naturally occur in the intra and extracellular spaces of all tissues and organs. Most have vital biological functions – like the metabolic cofactors NAD(P)H and FAD+, as well as the structural protein collagen. Others have been considered to be waste products – like lipofuscin and advanced glycation end products – which accumulate with age and are associated with cellular dysfunction. Due to their natural fluorescence these materials have great utility for enabling non‐invasive, label‐free assays with direct ties to biological function. Numerous technologies, with different advantages and drawbacks, have been applied to their assessment, including fluorescence lifetime imaging microscopy, hyperspectral microscopy, and flow cytometry. Here, we review the applications of label‐free autofluorophore assessment for clinical and health‐research applications, with specific attention to biomaterials, disease detection, surgical guidance, treatment monitoring and tissue assessment – fields which greatly benefit from non‐invasive methodologies capable of continuous, in vivo characterisation.This article is protected by copyright. All rights reserved