The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short nucleotide deletions and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Overall, our study highlights the comprehensive and clear picture of IR effects on normal mammalian genomes.