Background: The phenotypic and genetic relationships between carotid intima-media thickness (CIMT) and estimated glomerular filtration rate (eGFR) or urinary albumin-creatinine ratio (ACR) were evaluated in Korean twins and families. Methods: We recruited 688 participants (296 individual twins and 392 singletons, age 30–74 years) who were without myocardial infarction and stroke among participants in the Healthy Twin Study. eGFR was calculated using the Chronic Kidney Disease Epidemiology Collaboration equation. CIMT was measured using B-mode carotid ultrasound. Covariates were sex, Framingham risk scores, alcohol use, exercise, BMI, high-sensitivity C-reactive protein and triglycerides. Quantitative genetic and linear mixed analyses were performed. Results: In adjusted models there were associations between kidney function and CIMT with [beta] estimates ranging from –0.022 to –0.032 between eGFR and CIMT, and from 0.042–0.060 between ACR and CIMT. The covariate-adjusted heritabilities for eGFR, ACR and composite CIMT were 0.75, 0.32 and 0.45, respectively (p < 0.001). The adjusted genetic correlation between eGFR and CIMT was from –0.20 to –0.28 (p < 0.05), whereas there was no genetic correlation between ACR and CIMT. Conclusion: Kidney function is a surrogate marker of carotid atherosclerosis and further studies of the pleiotropic relationships between CIMT and eGFR are warranted.