Targeting metabolic syndrome (MetS) in early chronic kidney disease (CKD) is essential to reduce cardiovascular complications. We compared the association of kidney function estimated by two glomerular filtration rate (GFR) equations with MetS in community population.We analyzed 12,700 participants from 2009 to 2010 the Korea National Health Survey data. GFR was estimated using the CKD Epidemiology Collaboration equation (GFR CKD-EPI ) and the Modification of Diet in Renal Disease study equation (GFR MDRD ).The prevalence of MetS increased from the highest GFR category (>105ml/min/1.73m 2 ) to the lowest (<60ml/min/1.73m 2 ) using both equations (GFR CKD-EPI , 14.1% to 62.3%; GFR MDRD , 18.4% to 62.9%). Participants reclassified to higher GFR CKD-EPI category (upward) from GFR MDRD had lower prevalence of MetS than those moved downward (Net reclassification improvement 13.7%, P<0.001). Compared with GFR ≥105ml/min/1.73m 2 , mildly impaired GFR CKD-EPI (75–89ml/min/1.73m 2 ) was independently associated with increased odds of MetS (OR 1.30, 95% CI 1.09–1.56, P=0.003) in multivariate analysis, whereas GFR MDRD was not (OR 1.08, 95% CI 0.92–1.27, P=0.344).Compared with GFR MDRD , GFR CKD-EPI showed better association with prevalence of MetS, particularly in normal to mildly impaired GFR range. GFR CKD-EPI may improve risk stratification of individuals with MetS according to kidney function in community-based population.