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Isocyanates are included into a class with an extreme commercial importance because their use in the manufacture of polyurethanes. Polyurethanes are used in several applications such as adhesives, coatings, foams, thermoplastics resins, printing inks, foundry moulds and rubbers. Agglomerated cork stoppers are currently used for still wines, semi-sparkle and gaseous wines, beer and cider. Methylene diphenyl diisocyanate (MDI) is presently the isocyanate used in the production of polyurethane based adhesive in use due to its lowest toxicity comparing with toluene diisocyanate (TDI) previously employed. However, free monomeric TDI or MDI, depending on the based polyurethane, can migrate from agglomerated cork stoppers to beverages therefore it needs to be under control. The presence of these compounds are usually investigated by HPLC with Fluorescence or UV-Vis detector depending on the derivatising agent. Ultra Performance Liquid Chromatography with Diode Array Detector (UPLC-DAD) method is replacing HPLC. The objective of this study is to determine which method is better to analyze isocyanates from agglomerated cork stoppers, essentially TDI to quantify its monomer. A Design of Experiments (DOE) with three factors, column temperature, flow and solvent, at two levels was done. Eight experiments with three replications and two repetitions were developed. Through an ANOVA the significance of the factors was evaluated and the best level’s factors were selected. As the TDI has two isomers and in this method these two isomers were not always separated an ANOVA with results of resolution between peaks was performed. The Design of Experiments reveals to be a suitable statistical tool to determine the best conditions to quantified free isocyanates from agglomerated cork stoppers to real foodstuff. The best level’s factors to maximize area was column temperature at 30ºC, flow to 0,3 mL/min and solvent 0,1% Ammonium Acetate, to maximize resolution was the same except the solvent that was 0,01% Ammonium Acetate.