Computed tomography represents the gold standard in forensic and palaeopathological diagnosis. However, the X-rays used may affect the DNA quality through fragmentation and loss of genetic information. Previous work showed that the effects of ionizing radiation on dry DNA are non-significant with P < 10−8, which cannot be detected by means of polymerase chain reaction methods. In the present paper, complete analytical model that characterizes radiation effects on fragmented DNA in dry, wet, and frozen states is described. Simulation of radiation tracks in water phantom cells was performed using the Geant4-DNA toolkit. Cell hits by electrons with energies between 5 and 20 keV were simulated, and the formation of radiolytic products was assessed at a temperature of 298 K. The diffusion coefficient and the mean square displacement of reactive species were calculated by Stokes–Einstein–Smoluchowski relations at 273 K. Finally, DNA fragment damage was estimated using the density distribution of fragments calculated from atomic force microscopy images. The lowest probability of radiation-induced DNA damage was observed for dry state, with a range from 2.5 × 10−9 to 7.8 × 10−12 at 298 K, followed by that for frozen state, with a range from 0.9 to 4 × 10−7 at 273 K. The highest probability of radiation-induced DNA damage was demonstrated for fragmented DNA in wet state with a range from 2 to 9 × 10−7 at 298 K. These results significantly improve the interpretation of CT imaging in future studies in forensic and palaeopathological science.