Background Although radiation therapy plays a central role in the management of prostate cancer, complications remain a troubling byproduct. We sought to determine the prevalence and significance of colorectal complications after external beam radiation (EBRT) versus brachytherapy (BT) for prostate cancer. Methods We performed a retrospective review of all patients undergoing EBRT or BT for prostate cancer from January 1999 to October 2005. Toxicities were graded using the Radiation Therapy Oncology Group scoring system or the modified Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer grading criteria. Results A total of 183 patients underwent EBRT and 50 patients underwent BT with a mean follow-up period of 39 months. BT was associated with significantly less acute (6% vs 43.5%) and late toxicities (2% vs 21.8%; both P < .001). Among patients receiving EBRT, acute grade 3 toxicity was experienced by 1 (.5%) patient, and grade 2 toxicity was experienced by 79 (43%) patients. Increased stool frequency was the most common manifestation (62%), followed by rectal pain and urgency (30%) and rectal bleeding (21%). Late toxicity included 34 (18.6%) patients with grade 2 toxicity (bleeding, 68%; frequent stools, 26%; pain and urgency, 18%), and 5 patients (2.7%) with grade 3 toxicity (bleeding requiring multiple cauterizations, 3; small-bowel obstruction requiring surgery, 1; anal stenosis requiring repeat dilations, 1). BT was relatively well tolerated, with only 3 patients (6%) experiencing grade 2 acute toxicity symptoms of pain and urgency. One BT patient suffered late grade 2 toxicity of bleeding requiring intervention. One patient developed rectal cancer 20 years after EBRT. Conclusions Despite its relative safety, radiation therapy for prostate cancer has a significant incidence of colorectal complications. Overall, BT has a significantly lower incidence of acute and late toxicities than EBRT.