Handling with genetically modified organisms (GMOs) is regulated namely in EC. Laboratories often use polymerase chain reaction (PCR) based screening methods to monitor the presence of GM particles in food commodities as a cost effective approach. The reliability was tested of such screening using 35S CaMV promoter as the target sequences. Soya grown from non-GM cultivar as declared by a seed company was investigated after the harvest, transport to the silo, and before processing. The results based on PCR and real-time PCR analysis clearly showed that, the contamination with debris of other species, dust during transport, storage, and other kind of handling led to contamination with detectable amounts of Cauliflower mosaic virus (CaMV). Impurities are allowed by EC regulations but may, as we have shown, interfere with the analytical procedures based on PCR. The identification of 35S CaMV promoter and NOS terminator in food with uncertain history and no approved specific events may indicate unknown GMOs and perhaps emergency situation.