Background Estimation of glomerular filtration rate (GFR) is limited by differences in creatinine generation among ethnicities. Our previously reported GFR-estimating equations for Japanese had limitations because all participants had a GFR less than 90 mL/min/1.73 m2 and serum creatinine was assayed in different laboratories. Study Design Diagnostic test study using a prospective cross-sectional design. New equations were developed in 413 participants and validated in 350 participants. All samples were assayed in a central laboratory. Setting & Participants Hospitalized Japanese patients in 80 medical centers. Patients had not participated in the previous study. Reference Test Measured GFR (mGFR) computed from inulin clearance. Index Test Estimated GFR (eGFR) by using the modified isotope dilution mass spectrometry (IDMS)-traceable 4-variable Modification of Diet in Renal Disease (MDRD) Study equation using the previous Japanese Society of Nephrology Chronic Kidney Disease Initiative (JSN-CKDI) coefficient of 0.741 (equation 1), the previous JSN-CKDI equation (equation 2), and new equations derived in the development data set: modified MDRD Study using a new Japanese coefficient (equation 3), and a 3-variable Japanese equation (equation 4). Measurements Performance of equations was assessed by means of bias (eGFR − mGFR), accuracy (percentage of estimates within 15% or 30% of mGFR), root mean squared error, and correlation coefficient. Results In the development data set, the new Japanese coefficient was 0.808 (95% confidence interval, 0.728 to 0.829) for the IDMS–MDRD Study equation (equation 3), and the 3-variable Japanese equation (equation 4) was eGFR (mL/min/1.73 m2 ) = 194 × Serum creatinine−1.094 × Age−0.287 × 0.739 (if female). In the validation data set, bias was −1.3 ± 19.4 versus −5.9 ± 19.0 mL/min/1.73 m2 ( P = 0.002), and accuracy within 30% of mGFR was 73% versus 72% ( P = 0.6) for equation 3 versus equation 1 and −2.1 ± 19.0 versus −7.9 ± 18.7 mL/min/1.73 m2 ( P < 0.001) and 75% versus 73% ( P = 0.06) for equation 4 versus equation 2 ( P = 0.06), respectively. Limitation Most study participants had chronic kidney disease, and some may have had changing GFRs. Conclusion The new Japanese coefficient for the modified IDMS–MDRD Study equation and the new Japanese equation are more accurate for the Japanese population than the previously reported equations.