Three PCR primer pairs suitable for common regulatory elements of genetically modified organisms (GMOs) were compared for selection the most effective screening method for GMO. Two of the primer pairs such as: 35S1/35S2 and 35S-cf3/35S-cr4 are specific to 35S promoter from Cauliflower Mosaic virus and one primer pair NOS1/NOS2 is specific to the NOS terminator from Agrobacterium tumefaciens. The Roundup Ready soybean was used as GM material. The comparison of the primer pairs was carried out in two different PCR conditions PCR1 and PCR2. The results obtained exhibited 35S promoter specific primer pair 35S-cf3/35S-cr4 as the most specific, sensitive and efficient tool for GMO screening in the both PCR conditions applied.