The isolation of DNA from foodstuffs is the first step in the detection of genetically modified organisms. Refining processes, however, have an irrevocable influence on the quality and quantity of DNA and make detection in refined oil impossible. In order to determine the most significant step in removing DNA from crude soybean oil, two refining processes were considered: chemical refining and physical refining. Although conducted on a lab scale, quality parameters showed that the refining processes were good simulations of the industrial refining. From samples drawn at various refining stages, DNA was extracted with a protocol originally developed for the extraction of DNA from lecithin. The polymerase chain reaction results prove that the protocol was sufficiently useful for extracting DNA from soybean oil. The amplified DNA revealed that degumming is the most important step in removing DNA from crude soybean oil. After degumming, DNA was concentrated in the water fraction; no DNA could be amplified in the oil fractions. During physical degumming, degradation of DNA was observed.