For indirect determination of 3-chloro-1,2-propanediol fatty acid esters (3-MCPDEs) and glycidyl fatty acid esters (GEs) in thermally processed foodstuffs distributed in Japan, we modified two published methods, an enzymatic method (later approved as JOCS Standard Method for the Analysis of Fats, Oils, and Related Materials 2.4.14-2016 and Joint JOCS/AOCS Official Method Cd 29d-19) and EFSA method developed by the Joint Research Centre of the European Commission. The performance of these methods was demonstrated to be satisfactory. The partially modified enzymatic method showed mean recoveries of 93.7-98.5% for 3-MCPDEs, 94.4-98.4% for GEs, and HorRat(r) values of 0.06-0.78 in analyses of 6 types of foods including Japanese specific foods (fried rice cracker, fried instant noodle, biscuit, karinto, vegetable tempura, and frozen deep-fried chicken) spiked with 3-MCPD dioleate and glycidyl oleate at 0.02-0.04 mg/kg or 0.2-0.4 mg/kg. The partially modified EFSA method showed mean recoveries of 96.6-99.4% for 3-MCPDEs, 95.7-100.1% for GEs, and HorRat(r) values of 0.14-1.05 in analyses of 5 types of foods (not including karinto) spiked simultaneously with 3-MCPD dioleate and glycidyl oleate at either 0.02-0.04 mg/kg or 0.2-0.4 mg/kg. The results of analyses of 9 samples (fried rice cracker, biscuit, 2 potato crisps, fried potato snack, baked cracker, cracker dough, seafood tempura, and frozen deep-fried chicken) using these 2 methods were comparable. The 95% confidence intervals determined with weighted Deming regression analysis between the results of 3-MCPDEs or GEs in the same samples analyzed by the 2 methods showed: the slope around 1 (3-MCPDEs, 0.982-1.025; GEs, 0.887-1.078); and intercept close to 0 (3-MCPDEs, -0.002-0.003; GEs, -0.011-0.015). These data confirmed that the concentrations of 3-MCPDEs and GEs in food samples determined by 2 independent analytical methods were equivalent.