Biotechnology helps to alleviate problems of insufficient food by introducing transgenic foodstuff. The existence of transgenic food in the market and the lack of information in food labeling indicating the product’s action, certification of origin, and the quality of foodstuff have required the development of powerful tools to detect the transgenic organisms in food. In this study the DNA’s integrity processed tomato food was evaluated. Preparation of tomato puree and ketchup were required to evaluate the influence of additives on the integrity, quality, and amplificability of genomic DNA of tomato to detect transgenic genes. Samples of fresh tomato were analyzed as positive control. The accD, LAT52, and PG amplicons indicated the presence of transgenic tomato fruits. The ingredients or acid additives and storage time were the most important factors that affected the detection of transgenes. The results confirmed that quality and integrity of the DNA extracts are very important to develop the molecular techniques for the detection of transgenes and food traceability.