Recent developments in microbeam technology have made drastic improvements in particle delivery, focusing, image processing and precision to allow for rapid advances in our knowledge in radiation biology. The unequivocal demonstration that targeted cytoplasmic irradiation results in mutations in the nuclei of hit cells and the presence of non-targeted effects, all made possible using a charged particle microbeam, results in a paradigm shift in our basic understanding of the target theory and other radiation-induced low dose effects. The demonstration of a bystander effect in 3D human tissue and whole organisms have shown the potential relevance of the non-targeted response in human health. The demonstration of delayed mutations in the progeny of bystander cells suggest that genomic instability induced following ionizing radiation exposure is not dependent on direct damage to cell nucleus. The identification of specific signaling pathways provides mechanistic insight on the nature of the bystander process.