The global increase in genetically modified organism (GMO) content in feed and food products has necessitated the development of precise detection methods to differentiate between biotechnologically derived foods and those without GMOs. Despite the various regulations in different countries, an internationally consistent approach to labeling GMO products is needed. For this reason, there is a widespread need to develop effective GMO detection methods to provide reliable and transparent food safety to consumers. The first experimental step in creating accurate and reliable detection methods for GMOs is effective DNA isolation. Determining DNA isolation methods specific to different processing levels of foods is very important. This study was aimed to compare different DNA extraction methods in biscuit samples. For this reason, DNA from different biscuit samples was isolated using three different protocols (CTAB-PVP, modified CTAB-1, and modified CTAB-2). DNA samples extracted from biscuits, were evaluated regarding DNA concentration and purity. According to the results obtained, the CTAB-2 procedure generally showed the best performance in terms of both DNA amount and purity rates for biscuit samples.