BACKGROUND: Left ventricular hypertrophy (LVH) is an independent predictor of cardiovascular disease in the general population and in patients with chronic kidney disease. The objective of this study was to investigate the association of estimated glomerular filtration rate (eGFR) with left ventricular mass index (LVMI), LVH and left ventricular geometry. A question of clinical relevance is whether estimated glomerular filtration rate based on cystatin C (eGFRcystatinC) is a better marker for cardiovascular risk than estimated glomerular filtration rate based on creatinine (eGFRcreatinine). METHODS: The study sample included 2830 individuals from the population-based Study of Health in Pomerania (SHIP). LVH was defined as echocardiographic LVMI >48 g/m(2.7) in men and >44 g/m(2.7) in women. Kidney function, as assessed by eGFR, was determined from established equations: the creatinine-based Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation and a cystatin-based multivariable equation. RESULTS: We found an inverse association between eGFR and LVMI. This association was stronger in models with eGFRcystatinC than in models with eGFRcreatinine. Subjects with moderately-to-severely decreased kidney function (defined as eGFR 15-<60 mL/min per 1.73 m(2)) had higher odds for abnormal geometric patterns of the left ventricle than subjects with normal eGFR when eGFRcystatinC was used. CONCLUSIONS: The findings suggest that eGFRcystatinC is superior to eGFRcreatinine for assessing the risk of cardiovascular disease.