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© The Author(s) 2017., Understanding the human brain is the ultimate goal in neuroscience, but this is extremely challenging in part due to the fact that brain tissue obtained from autopsy is practically the only source of normal brain tissue and also since changes at different levels of biological organization (genetic, molecular, biochemical, anatomical) occur after death due to multiple mechanisms. Here we used metabolomic and anatomical techniques to study the possible relationship between post-mortem time (PT)-induced changes that may occur at both the metabolomics and anatomical levels in the same brains. Our experiments have mainly focused on the hippocampus of the mouse. We found significant metabolomic changes at 2 h PT, whereas the integrity of neurons and glia, at the anatomical/ neurochemical level, was not significantly altered during the first 5 h PT for the majority of histological markers., This work was supported by grants from the following entities: the Spanish Ministerio de Economía y Competitividad (Grants CTQ2014-55279-R to CB and AG and Grant SAF 2015-66603-P to JD); the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 720270 (Human Brain Project) to JD; and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED, CB06/05/0066, Spain) to JD. CGR was awarded a research fellowship from the University CEU San Pablo.