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Genetically modified organisms have become a part of our environment and food chain. Roundup Ready soybean is at the moment the most frequent one that man can meet. National regulations require careful monitoring and detection of GMOs. We present in this investigation comparison of several protocols and individual steps, which are included in the whole detection procedure. Currently used CTAB based protocol is suitable for DNA isolation from the green plant tissue but also from the flour. Lectin coding sequence specific primers were suitable for soybean DNA detection unlike leu-tRNA gene specific primers. Only one of the tested CaMV sequence specific primer pairs did not amplify unspecific products under condition tested. NOS terminator specific primer pair was found suitable for routine screening. EPSPS gene was detected using two different protocols; the same primers did not identify other Roundup Ready GM crops.