Abstract Corn is one of the most important economic, social and cultural agricultural products in Paraguay, being the main ingredient of several typical foods. Due to the cross-pollination of this plant, it can be contaminated with transgenic maize pollen found in nearby fields. The general objective of this research was to evaluate the presence of transgenic sequences in corn grains marketed in the Departments of Itapúa, Alto Paraná and Canindeyú for the preparation of flour for human consumption. We studied 18 samples of corn kernels marketed for the preparation of flour from the Departments of Itapúa, Alto Paraná and Canindeyú. The DNA was extracted using the Trimethyl Ammonium Bromide (CTAB) protocol. For the detection of the transgenic sequences, the polymerase chain reaction (PCR) method was used. The bands were analyzed visually and using the ImageJ program. The results showed the presence of 5 positive samples for the P-35S-CaMv promoter and 5 samples for the T-nos terminator, none of them presented both sequences sought in the same construction; this indicates that 10 of 18 samples were contaminated with transgenic sequences. These findings show that transgenic products are available in Paraguayan local markets without consumers being aware of this situation.