Analytical methods based on the polymerase chain reaction (PCR) technology are increasingly used for the detection of deoxyribonucleic acid (DNA) sequences associated with genetically modified organisms (GMOs). Prerequisites for GMO detection are a minimum amount of the target gene and prior knowledge of the type of genetic modification, such as virus or insect resistance traits, including controlling elements (promoters and terminators). Moreover, DNA extraction and purification is a critical step for the preparation of PCR-quality samples, particularly for processed agricultural crops. This paper will review the state-of-the-art of PCR method development for the qualitative and quantitative determination and identification of GMOs, and will include a short summary of official and validated GMO detection methods.