Background Existing creatinine-based equations to estimate glomerular filtration rate (GFR), developed primarily in populations of European and African American ancestry, do not accurately reflect the GFR in the Indian population due to differences in body composition, diet, and other factors. This manuscript describes the rationale and methodology for developing a creatinine-based equation for more accurate GFR estimation in Indian subjects. Materials and Methods This cross-sectional study will be conducted in India’s two geographically and demographically diverse locations: Chandigarh (north) and Puducherry (south). Participants will include a representative sample from the general population and subjects with chronic kidney disease (CKD), with the latter being recruited from outpatient clinics. A total of 1558 subjects will be enrolled in the discovery and cross-validation cohort and 620 subjects in the external validation cohort. The reference standard for measured GFR (mGFR) will be the plasma clearance of iohexol. Stepwise multiple regression on log-transformed data will determine a set of variables that jointly predict mGFR and identify factors influencing mGFR and estimated (eGFR) in the study population. This study will also explore the performance of mGFR by iohexol measurement from dried blood spots against mGFR from plasma clearance of iohexol. Conclusion Developing a more reliable and accurate creatinine-based GFR estimating equation will improve CKD diagnosis, classification, and management. The findings will have substantial implications for CKD research in India and other regions with similar populations.