An improved routine, simple and sensitive method is presented for the determination of free and bound 3-chloropropane-1,2-diol (3-MCPD) in different foods using capillary gas chromatography with mass spectrometric detection and deuterated 3-MCPD as internal standard. The optimised method was linear within the working calibration standard concentrations in the range of 0.009–1.3 mg 3-MCPD per 1 kg of sample. The LOD and LOQ were 0.003 µg/kg and 0.009 µg/kg, respectively. Validation of the method was carried out by analysing standards of
3-MCPD, acid-HVP, roasted coffee samples, and the same samples spiked with 3-MCPD. Repeatability (expressed as RSD) of the method was in the range 1.0–4.2%, the average spike recoveries were 99.1–99.5% (RSD = 0.8–1.4%), respectively. 3-MCPD bound in esters with higher fatty acids was isolated as fat, the isolated fat was subjected to methanolysis and 3-MCPD generated was quantified using the same method. The LOD and LOQ were determined to be 1.1 mg/kg of lipids and 3.3 mg/kg of lipids, respectively. Using the optimised method, 20 samples of retail food products were analysed for their free and bound 3-MCPD. All samples contained free 3-MCPD at 9.6–83 µg/kg (RSD = 0.4–7.0%). The level of the bound 3-MCPD varied between the LOD and 2.4 mg/kg with RSD = 0.3–2.4%.