Background: Effects of stroke at the cellular and sub-cellular level remain poorly understood by conventional techniques. We use synchrotron-based imaging techniques to study elemental and biochemical changes in the infarct and penumbra after stroke in an experimental model. Methods: Ischemic stroke is induced in mice using the previously validated photothrombotic model. Animals are sacrificed at various time-points after stroke. Fourier transform infrared spectroscopic imaging (FTIRI) is used to gather sub-cellular (<1 µm spatial resolution) imaging data of lipid oxidation and protein aggregation in the areas of interest. X-ray fluorescence (XRF) imaging is used to image the distribution of bio-important elements at the cellular and sub-cellular spatial resolutions. Routine histology and immunohistochemistry are used to co-localize cell-types to areas of interest. Results: Preliminary XRF results indicate significant reduction in the concentration of multiple elements in the infarct, compared to the penumbra, at day 1 post-stroke. Some elements begin to return to normal concentration in the penumbra at day 3. FTIRI data shows that lipid and total protein levels decrease, while aggregate protein levels increase in the penumbra. Conclusions: Multi-modality synchrotron imaging can be used to map elements as well as bio-molecules in a stroke model. A better understanding of these changes can guide therapeutic interventions after stroke.