Background: chronic kidney disease (CKD) diagnosis relies on glomerular filtration rate (eGFR) estimation, traditionally using the creatinine-based Modification of Diet in Renal Disease (MDRD) equation. The Chronic Kidney Disease Epidemiology Collaboration (CKDEPI) equation performs better in estimating eGFR and predicting mortality and CKD progression risk. Cystatin C is an alternative glomerular filtration marker less influenced by muscle mass. CKD risk stratification is improved by combining creatinine eGFR with cystatin C and urinary albumin to creatinine ratio (uACR). We aimed to identify the impact of introducing CKDEPI and cystatin C on the estimated prevalence and risk stratification of CKD in England and to describe prevalence and associations of cystatin C. Methods and findings: cross sectional study of 5799 people in the nationally representative 2009 and 2010 Health Surveys for England. Primary outcome measures: prevalence of MDRD, CKDEPI and cystatin C-defined eGFR60ml/min/1.73m2 with albuminuria (CKD Category G1-2) reclassified almost a tenth into a higher risk group. Limitations: cross sectional study, single eGFR measure, no measured (‘true’) GFR. Conclusions: introducing the CKDEPI equation and targeted cystatin C measurement reduces estimated CKD prevalence and improves risk stratification