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The generation, manipulation and quantification of non-classical light, such as quantum-entangled photon pairs, differs significantly from methods with classical light. Thus, quantum measures could be harnessed to give new information about the interaction of light with matter. In this study we investigate if quantum entanglement can be used to diagnose disease. In particular, we test whether brain tissue from subjects suffering from Alzheimer’s disease can be distinguished from healthy tissue. We find that this is indeed the case. Polarization-entangled photons traveling through brain tissue lose their entanglement via a decohering scattering interaction that gradually renders the light in a maximally mixed state. We found that in thin tissue samples (between 120 and 600 micrometers) photons decohere to a distinguishable lesser degree in samples with Alzheimer’s disease than in healthy-control ones. Thus, it seems feasible that quantum measures of entangled photons could be used as a means to identify brain samples with the neurodegenerative disease.