Atomic bomb (A-bomb) radiation is associated with cardiovascular disease (CVD) and metabolic CVD risk factors. Chronic kidney disease (CKD) is also known to be a risk factor for CVD and little is known whether CKD is associated with A-bomb radiation. To examine whether CKD is associated with CVD risk factors or with A-bomb radiation in A-bomb survivors, we classified renal dysfunction in 1,040 A-bomb survivors who were examined in 2004–2007 as normal [n = 121; estimated glomerular filtration rate (eGFR) ≥90 ml/min/1.73 m²]; mild (n = 686; eGFR 60–89 ml/min/1.73 m²); moderate (n = 217; eGFR 30–59 ml/min/1.73 m²); or severe (n = 16; eGFR <30 ml/min/1.73 m²). Also, we diagnosed subjects in the moderate and severe renal dysfunction groups as having CKD (n = 233; eGFR <59 ml/min/1.73 m²). After adjusting for age, gender, and smoking and drinking habits, we looked for an association between renal dysfunction and hypertension, diabetes mellitus (DM), hyperlipidemia, and metabolic syndrome (MetS), and between renal dysfunction and A-bomb radiation. Hypertension [odds ratio (OR), 1.57; 95% confidence interval (CI), 1.12–2.20, P = 0.009]; DM (OR, 1.79; 95% CI, 1.23–2.61, P = 0.002); hyperlipidemia (OR, 1.55; 95% CI, 1.12–2.14, P = 0.008); and MetS (OR, 1.86; 95% CI, 1.32–2.63, P < 0.001) were associated with CKD (moderate/severe renal dysfunction), and hyperlipidemia and MetS were also associated with mild renal dysfunction. CKD (OR/Gy, 1.29; 95% CI, 1.01–1.63, P = 0.038) and severe renal dysfunction (OR/Gy, 3.19; 95% CI, 1.63–6.25, P < 0.001) were significantly associated with radiation dose. CKD associated with radiation may have played a role in the development of CVD among A-bomb survivors.