The fate of DNA during steeping, wet-milling, and subsequent processing of maize was examined using a sensitive polymerase chain reaction (PCR-based) detection system. The system used specific amplification of maize DNA sequences by primers generated toward plant nuclear- and chloroplast-encoded genes. The PCR method facilitated analysis of DNA content in food products, which is an important issue in use of genetically modified organisms. In a conventional laboratory wet-milling countercurrent steep system, DNA was detected in maize kernels throughout the process but was not found in steepwater. After kernels were wet-milled DNA' was detected in the starch, germ, coarse fiber, and wet gluten fractions but not in the fine fiber fraction. When dried by heating at 135°C for 2 hr, DNA was degraded to undetectable levels in the wet-milled gluten fraction and hydrated kernels. DNA was not detected in feed pellets, starch, dextrose, sorbitol, or high-fructose maize syrup made from industrial wet-milled samples. Although DNA could be detected in laboratory wet-milled fractions, some degree of degradation occurred after extended exposure to steepwater. Countercurrent steepwater samples from the later stages of the steeping process were able to degrade DNA. The level of DNA degradation appeared to correspond to the presence of sulfur dioxide and may represent a physiochemical rather than an enzyme-mediated process. Our results indicate that some steps in the steeping and wet-milling process can degrade maize genomic and plastid DNA.