Mitochondrial aldehyde dehydrogenase 2 (ALDH2) is a key enzyme involved in alcohol metabolism. Variants in ALDH2 are associated with increased risks of cardiovascular disease, hypertension, and heart failure with preserved ejection fraction. However, the relationship between ALDH2 variants (GG, GA, and AA) and chronic kidney disease (CKD) remains uncertain. This study aimed to investigate the incidence of CKD according to ALDH2 alleles. We analyzed 5,369 individuals without CKD from the Korean Genome and Epidemiology Study (KoGES). This prospective, community-based cohort consists of middle-aged Koreans (40–69 years old), residing in specific regions of South Korea. Participants were followed up every two years through health surveys and standardized protocols. A multivariable Cox proportional hazards regression was performed to assess the independent association of ALDH2 polymorphisms with incident CKD. CKD was defined as an estimated glomerular filtration rate (eGFR) <60 mL/min or proteinuria ≥1+ on two consecutive measurements ≥90 days apart. Covariates included age, sex, diabetes, hypertension, hyperlipidemia, smoking history, alcohol consumption, education, baseline eGFR, hemoglobin, income and physical activity. Among participants, 2,580 (48.05%) were men, and 3,301 (61.48%) were less frequent drinkers. The minor allele frequency (GA+AA) was 1,551 (28.88%). CKD incidence was 26%. The hazard ratio (HR) for CKD in GA+AA vs. GG was 1.07 (95% CI, 0.95–1.30), showing no significant association. Separate analyses of GG and GA+AA showed no CKD difference across alcohol consumption levels. No significant differences were found after stratification by sex and alcohol intake. ALDH2 polymorphisms did not influence CKD occurrence, regardless of sex and alcohol intake. Drinking behavior by ALDH2 genotype also had no effect. These findings suggest that ALDH2 variants and alcohol consumption are not major CKD risk factors.