Chronic kidney disease (CKD) is characterized by a reduced glomerular filtration rate (GFR) and proteinuria. Modifiable lifestyle factors such as smoking and alcohol contribute to CKD. Recent cohort studies have shown that moderate alcohol consumption attenuates the decline of the GFR and smoking has been previously shown to be associated with CKD. However, the association of smoking and alcohol consumption on CKD is not entirely clear. To examine whether there is evidence to assume that smoking is an effective modifier of the association between CKD and alcohol consumption, we conducted a cross-sectional study of a population of people who presented for a health checkup under a program that targets the insured population aged ≧ 40 years using data from the Specific Health Check and Guidance in Japan between April 2008 and March 2009. Of the 506 807 participants aged ⩾ 40 years, 292 013 (57.6%) were included in the present analysis. Outcomes were kidney dysfunction, as an eGFR of o60 ml/min/1.73 m 2 , and proteinuria. In nonsmokers, drinking a small amount was associated with a lower prevalence of proteinuria, but in smokers, the association between alcohol and proteinuria was not observed. The analysis regarding eGFR o60 ml/min/1.73 m 2 revealed that in both smokers and nonsmokers, alcohol consumption was inversely associated with the risk of CKD. Mild to moderate alcohol consumption might be associated with a lower risk of CKD (proteinuria and eGFR), especially among nonsmokers, because smoking might have modified the potential benefits of alcohol to prevent CKD.