OBJECTIVES: To assess whether chronic kidney disease of unknown aetiology (CKDu) is present in India and to identify risk factors for it using population-based data and standardised methods. DESIGN: Secondary data analysis of three population-based cross-sectional studies conducted between 2010 and 2014. SETTING: Urban and rural areas of Northern India (states of Delhi and Haryana) and Southern India (states of Tamil Nadu and Andhra Pradesh). PARTICIPANTS: 12 500 individuals without diabetes, hypertension or heavy proteinuria. OUTCOME MEASURES: Mean estimated glomerular filtration rate (eGFR) and prevalence of eGFR below 60 mL/min per 1.73 m2 (eGFR <60) in individuals without diabetes, hypertension or heavy proteinuria (proxy definition of CKDu). RESULTS: The mean eGFR was 105.0±17.8 mL/min per 1.73 m2. The prevalence of eGFR <60 was 1.6% (95% CI=1.4 to 1.7), but this figure varied markedly between areas, being highest in rural areas of Southern Indian (4.8% (3.8 to 5.8)). In Northern India, older age was the only risk factor associated with lower mean eGFR and eGFR <60 (regression coefficient (95% CI)=-0.94 (0.97 to 0.91); OR (95% CI)=1.10 (1.08 to 1.11)). In Southern India, risk factors for lower mean eGFR and eGFR <60, respectively, were residence in a rural area (-7.78 (-8.69 to -6.86); 4.95 (2.61 to 9.39)), older age (-0.90 (-0.93 to -0.86); 1.06 (1.04 to 1.08)) and less education (-0.94 (-1.32 to -0.56); 0.67 (0.50 to 0.90) for each 5 years at school). CONCLUSIONS: CKDu is present in India and is not confined to Central America and Sri Lanka. Identified risk factors are consistent with risk factors previously reported for CKDu in Central America and Sri Lanka.