A study of the fragments of DNA irradiated with MeV ions is important for the understanding of the DNA damage mechanism and the subsequent biological effects (induced by heavy ions). In this experiment, the products of calf thymus DNA (CT DNA) irradiated with MeV fluorine ions were analyzed using agarose gel electrophoresis,modified time-of-flight mass spectrometer (MALDI-TOF), and high-performance liquid chromatography (HPLC).The results showed that the molecular mass of the fragments were concentrated around 831 bp with agarose gel electrophoresis, there was no observable product in the range of 1,000- 30,000 (m/q) using MALDI-TOF, and small biomolecules were separated from the products. The results of this study indicated that the strand breaks of calf thymus DNA induced by MeV fluorine ions were nonrandom.