Temperature and pH are important parameters in food processing. Their effect on degradation of plasmid and plant DNA was investigated. Application of HPLC permitted us to quantitatively distinguish between covalently closed circular and nicked plasmid DNA. Nicking of plasmid DNA in buffer increased strongly at decreased pH (99% within 90 min at 65 °C/pH 4.0). A virtually identical degradation rate was observed in tomato serum. Temperature exerted only minor effects (15% within 90 min at 85 °C/pH 8.4). The combined effect of the parameters was additive. Degradation of plant DNA was monitored by determining the maximal detectable fragment length using polymerase chain reaction. With transgenic maize DNA in buffer, fragments up to 957 bp remained detectable for at least 90 min upon application of 65 °C at pH 4.0. Soymilk and tofu were produced from genetically modified soybeans. After boiling (10 min) of raw soymilk, the detectable fragment length decreased from 1,714 to 1,339 bp. The study of the final tofu product did not reveal any further DNA degradation. In commercial soy protein isolate, a rather highly processed food, DNA fragments of at least 714 bp were detected.