Glycidyl esters are foodborne contaminants formed during the production of fats and oils, especially during the deodorization of palm oil. The hydrolyzed free form of glycidol has been categorized as probably carcinogenic to humans by the World Health Organization’s International Agency for Research on Cancer. The aim of this research was to study the formation of glycidyl esters during the lab-scale deodorization of the three most widely produced seed oils in the world (sunflower, rapeseed and soybean). The effects of two independent factors – temperature and residence time – were analyzed by a 32 full factorial experimental design and evaluated by response surface methodology. In accordance with findings in the literature, the greatest amount of glycidyl esters was formed in the soybean oil matrix. For all three oils, the effects of both residence time and temperature were significant, while the latter was more so. To reduce the formation of glycidyl esters, milder deodorization is required, which is limited because of the purposes sought by the thermal operation and removal of volatile minor components and contaminants.