Both gas chromatography-mass spectrometry in electron ionization (GC-MS-EI) and negative chemical ionization (GC-MS-NCI) modes are reported in this paper for the simultaneous determination of 1,3-dichloropropan-2-ol (1,3-DCP), 2,3-dichloropropan-1-ol (2,3-DCP), 3-chloropropane-1,2-diol (3-MCPD) and 2-chloropropane-1,3-diol (2-MCPD) in soy sauce and other flavoring. D(5)-3-MCPD (for 3-MCPD and 2-MCPD) and d(5)-1,3-DCP (for 1,3-DCP and 2,3-DCP) were used as the deuterium isotopic labelled internal standards. The feasibility of using heptafluorobutyric anhydride modified with triethylamine (HFBA-Et(3)N) as a new derivatization reagent to replace heptafluorobutyrylimidazole (HFBI) is proposed. Liquid/liquid extraction with hexane was introduced for high lipid content samples. A small survey was carried out of soy sauces (103 samples) and instant noodles (45 samples) and the applicability of GC-MS-NCI and GC-MS-EI was assessed in these different matrices.