Precise geometry and reduced scattering makes synchrotron radiation a convenient tool for studying non-targeted effects of radiation, such as the bystander and abscopal effect. We investigated these effects using microbeam radiation therapy (MRT) and conventional broadbeam (BB) radiation. MRT is a promising novel tumour-treatment modality for delivering synchrotron radiation through a collimator, resulting in a lattice of planar radiation microbeams. When compared with BB radiation, MRT yields improved therapeutic benefits, particularly towards preserving healthy tissues. To establish if these effects depend on the dose, irradiated volume, and time post-irradiation, C57BL/6 mice were MRT- and BB-irradiated at the Australian Synchrotron’s Imaging and Medical Beamline with either 10Gy or 40Gy peak doses in 8x8, 8x1 or 2x2mm localised areas on their right-hind thigh. Here we describe our experimental approach to study the local immune response in healthy mouse tissues, following localised irradiation. Irradiated skin was collected at 24 hours and 96 hours post-irradiation and processed for immunohistochemical analysis of apoptotic cells and modulators of innate and adaptive immune response. Activated macrophages (F4/80-positive cells) yielded statistically significant increases across both MRT and BB radiation areas, with maximal increases up to 3.1 fold for higher combined dose and irradiated area values (Gy x mm). Neutrophils (Ly-6G-positive cells) showed increases of statistical significance predominantly across BB conditions, up to 1.8 fold. T-lymphocytes (CD3-positive cells) yielded no statistically significant changes relative to the unirradiated skin. These results show that following a minor pulsed exposure of synchrotron radiation, there appears to be a persistent local innate immune response in mouse skin, whilst the adaptive immunity appears unresponsive. Parallel studies have shown this local immune response can cause genotoxic stress in non-targeted tissues. Our future experiments aim to study these immune response modulators in bystander tissues, including skin distant from the irradiated area, and intestine.