Oil refining is essential for ensuring quality and safety of oils and fats. However, during the deodorization step of the refining process, the oil is exposed to high temperatures and changes in the lipid matrix may occur leading to the formation of 3-chloropropane-1,2-diol (3-MCPD) esters and possibly other processing by-products. This study was initiated to address the limited understanding on the formation of 3-MCPD ester in oil refining. The impact of refining conditions, both at pilot-plant and industrial scale, were investigated by subjecting palm and rapeseed oils to different refining treatments. The experiments showed that 3-MCPD esters and glycidyl esters were formed during the deodorization of palm oil, but not rapeseed oil. The level of 3-MCPD esters in the refined palm oils (3.5–4.9 mg/kg) was independent of the deodorization conditions. No correlation was found between the level of 3-MCPD esters formed and the content of the potential precursors, partial acylglycerols and chlorides. In contrast, the formation of glycidyl esters was affected by the deodorization conditions (both temperature and residence time). Higher levels of glycidyl esters (up to 3.8 mg/kg) were found in palm oil deodorized at temperatures above 230°C.