Caudal protrusion of pelvic organs and dilatation and deviation of the rectum with perineal hernia (PH) have not previously been studied using CT, and it is not known how completely the changes normalize after PH repair. Objectives of this prospective experimental case series were to evaluate the dimensions and shape of the rectum and the volume, location, and other features (enhancement pattern, presence of cysts, and mineralizations) of the prostate of 66 dogs on CT before and 3 months after PH repair. The rectal cross‐sectional areas were measured at intrapelvic and caudal locations, and the shape was categorized as straight, deviated, flexure, or caudal fold on dorsal images. According to paired samples t‐tests, the caudal rectal dimensions were significantly larger (P < .001) than the intrapelvic dimensions both before and 3 months after PH repair, and according to linear mixed models, the intrapelvic dimensions increased significantly (P < .001) after repair. Before PH repair, the most common rectal shape was flexure (69.2%); after repair, the number of dogs having a straight rectum increased significantly (P < .001) according to the McNemar paired‐samples proportion test. We were also able to show that rectal dimensions increased after PH repair despite straightening in most dogs. According to the linear mixed model, prostate ratio volume, and according to Wilcoxon signed ranks test, the number of prostates with intraprostatic cysts decreased significantly (both P < .001) after PH repair, but the proportion of prostates located in the caudal or perineal area did not. Small mineralizations remained in some dogs.