Assessment of contamination of foods with monochloropropanediols (MCPD) and subsequent mitigation of their formation is an important current issue of a global food security. Methods for the determination of 2- or 3-MCPD in foods at low μg/kg levels require analyte derivatization prior to gas chromatography-mass spectrometry (GC-MS) determination. All existing methods suffer from various drawbacks associated with current derivatization schemes. We have developed a new derivatization scheme, which uses cyclohexanone as a derivatization agent and a sulfonated polymer as a solid-phase acidic catalyst. This derivatization uses a readily available derivatization reagent and does not require any postderivatization workup. The respective 2-MCPD 1,3-dioxane and 3-MCPD 1,3-dioxolane derivatives are stable with storage, produce characteristic molecular ions, and chromatograph well on nonpolar GC columns. This derivatization procedure was applied to the analysis of free 2- and 3-MCPD, bound 2- or 3-MCPD (in the form of fatty acid esters after acidic hydrolysis), and also to simultaneous analysis of free and bound forms. The method was tested on soy sauce, commercial palm oil, palm oil noodles from an instant soup, and olive oil, which was spiked with bound 2- and/or 3-MCPD. The results obtained using derivatization with cyclohexanone agreed with the data obtained using traditional heptafluorobutyryl imidazole derivatization. Additionally, data for soy sauce and palm oil matrices obtained through interlaboratory testing programs had z-scores <1. The method detection limit is 1–3 μg/kg for free 2- and 3-MCPD (sample weight dependent) and 100 μg/kg per fat for bound 2- and 3-MCPD.