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Summary: This study aimed to determine the best lipid extraction method for infant formula; therefore, it can be used as a routine analysis. The samples were some commercial infant formulas in Indonesia. The research was conducted with three steps: (i) Lipid extraction of infant formula using five lipid extraction methods; (ii) 3‐monochloropropanediol esters (3‐MCPDE) and glycidyl esters (GE) analysis of lipid extract from three lipid extraction methods in the first step; and (iii) 3‐MCPDE and GE analysis of six commercial infant formulas using the best lipid extraction method. The results showed that lipid extraction using the Dubois method gave the best results than other lipid extraction methods. The level of 3‐MCPDE and GE also had no significant difference with the addition of NaCl in the Folch method, compared with the addition of Na2SO4. The level of 3‐MCPDE and GE using the Dubois method was significantly different and higher compared with the other lipid extraction methods. 3‐MCPDE and GE levels of commercial infant formula were 6.62–52.84 µg kg−1 and <1.43–17.06 µg kg−1, respectively. The values obtained were still within the standard according to Commission Regulation EU 2018/290 by the European Food Safety Authority (125 µg kg−1 for 3‐MCPDE (on progress) and 50 µg kg−1 for GE). [ABSTRACT FROM AUTHOR]