DNA fragmentation, detected by microgel electrophoresis of single cells, is applied as a marker for irradiation treatment of seeds. Seeds may be treated with ionising radiation for the purpose of insect disinfestation or microbial control. Various seeds treated with radiation doses in the range of 0–5 kGy were analysed. After electrophoresis, irradiated cells—with a large number of DNA strandbreaks—showed tailing and appeared as distinct comets, whereas non-irradiated cells appeared nearly circular or with only slight comet tails. Shape, length and intensity of comets were dose-dependent. Although DNA comet assay has now been adopted as an official European Standard (EN 13784) to detect irradiated foodstuffs, the method discloses several limitations. Identification was successful for buckwheat, linseed, melon, nigella, poppy, sesame and sunflower seeds, but caused problems for fennel, fenugreek, millet and mustard seeds. In some foods, many comets were also detected in the non-irradiated samples, mimicking an irradiation treatment. The use of the DNA comet assay as a screening method for irradiated food, therefore, has its restraints, but for a number of foods it serves as a rapid and inexpensive test.