Synchrotron-generated microbeam radiation therapy (MRT) is a novel, preclinical tumour treatment modality. It has a unique ability to generate less radiation damage to neighbouring normal tissues compared to the conventional Broad Beam (BB) modality. A comprehensive investigation on the mechanisms and side effects of these modalities has currently not been established. Here we studied the radiation-induced bystander effect (RIBE) in vivo (or abscopal effect) induced by BB and MRT irradiation, generated by the Imaging and Medical Beamline (IMBL) at the Australian Synchrotron. C57BL/6 mice were irradiated with 10 Gy or 40 Gy of BB or MRT peak dose, in an 8x8, 8x1 and 2x2 mm area on the right hind leg, using an X-ray beam with a dose rate of 49 Gy/sec. At 24 and 96 hrs post-irradiation, we collected irradiated skin and an assortment of unirradiated tissues. As an endpoint, we measured the levels of two types of DNA damage. DNA double stranded breaks (DSB) were detected using the γH2AX assay in irradiated skin, distant skin (2cm away) from irradiated site, and in small intestine. Oxidative clustered DNA lesions (OCDL) were measured by constant gel electrophoresis in genomic DNA extracted from a variety of non-targeted tissues that was treated with purine, pyrimidine and abasic site-specific enzymes. For both radiation modalities the levels of γH2AX foci in non- targeted skin and intestine of irradiated mice varied in comparison to unirradiated control animals. Overall, MRT and BB induced an elevated γH2AX response at 10 Gy, while inhibiting this response at 40 Gy. We found a marked increase of all types of OCDLs in a variety of non-targeted tissues. We will discuss the role of irradiated volume, dose, and beam modality in the induction and manifestation of the in-vivo non-targeted effects.