Several methods to measure cell cycle perturbation after exposure to ionizing radiation are presented in this chapter. These methods include the G1 checkpoint assay by 5′ bromode-oxyuridine (BrdUrd) labeling followed by flow cytometric analysis, the S-phase checkpoint assay by measuring DNA synthesis in response to ionizing radiation, and the G2/M checkpoint assay by quantitating histone H3 phosphorylation after ionizing radiation.