The aim of the present study was to assess and quantify changes in the structural components of the rectal wall after irradiation with varying single doses of x-rays. A total of 70 CDF1/Bom male mice were irradiated at a selective 1.5 cm of the distal rectum with varying single doses of 0–30 Gy. At 32 weeks postirradiation the mice were sacrificed and the rectum was removed. Sampling of the specimens was based on unbiased stereological principles using systematic random sampling. Vertical tissue sections were used to estimate mucosal surface area density and to measure the thickness and volume fraction of the different intestinal wall layers. The surface area density decreased with increasing dose (p<0.02) due to pronounced injury of the crypts and mucosal morphology. The thickness and the volume fraction of the submucosa were significantly increased in the 20, 25 and 30 Gy treatment groups (p<0.0001 and p<0.0001), whereas the thicknesses of the mucosa, the lamina muscularis propria and the serosa did not change after irradiation. It is concluded that irradiation causes histopathological changes in the rectal mucosa and submucosa, and changes in the thickness of the submucosal intestinal layer. These changes were found to be dose-dependent.