Processing of raw plant materials causes occurrence of degraded DNA in foods. The effect of DNA degradation on amplification and quantification of transgenic and non-transgenic DNA in raw and experimentally thermally processed foods was studied. The degree of DNA degradation was checked by agarose gel electrophoresis and polymerase chain reaction (PCR). Cetyl trimethyl ammonium bromide method yielded DNA of a better quality, while Genespin and Wizard were less appropriate. Baking at 220°C considerably reduced the size of DNA fragments. In order to measure the length of amplifiable DNA, primers for soybean and maize genes were used. Small DNA fragments ranging from 100 to 200 bp were amplified in all samples. DNA fragments over 1 kbp were amplified only if heating at 220°C lasted less than 30 min. Baking of flour (220°C) reduced the size of extracted DNA fragments so that 1,100 bp amplicon was no longer amplifiable, while the amplicons of 913 and 1,100 bp were obtained from the baked bread. When PCR assays targeting maize high mobility group and zein genes were used under the same conditions, analogous results were achieved. Quantification of genetically modified organism content was not influenced by baking.