Background: Stereotactic body radiosurgery (SBRT) is a recent innovation in the treatment of prostate cancer that has begun to disseminate into national practice. Comparative studies have yet to be performed and little is known about the cost to Medicare or difference in toxicity between SBRT and intensity modulated radiation therapy (IMRT). Methods: We performed a retrospective study using a national sample of all Medicare beneficiaries age 66 or older who received SBRT or IMRT as primary treatment for prostate cancer during 2008 through 2011. Each SBRT patient was matched to two IMRT patients with similar follow-up (6, 12, or 24 months) and clinical and demographic characteristics. Cost of treatment was calculated for matched patients with six months of follow-up. We assessed toxicity by searching Medicare claims for procedure or diagnosis codes indicative of treatment related toxicity. We used a random effects model to compare the likelihood of genitourinary (GU), gastrointestinal (GI), and other toxicity from 0 to 6, 0 to 12, and 0 to 24 months after the initiation of SBRT or IMRT treatment. Results: The study sample consisted of 1,335 SBRT patients matched to 2,670 IMRT patients. The mean cost of SBRT was $11,668 compared to $15,838 for IMRT. At all follow-up points, SBRT patients were significantly more likely to experience GU toxicity. In the first six months after treatment initiation, 15.6% of SBRT versus 12.6% of IMRT patients had claim indicative of a GU complication (p=.009). In the first 12 months, 27.1% of SBRT versus 23.2% of IMRT had a GU complication (p=.014). Finally, from 0-24 months, 43.9% of SBRT versus 36.3% of IMRT had a GU complication (p=.001). The higher rate of GU toxicity after SBRT was largely due to an increase in urethral strictures and bladder outlet obstructions and urinary incontinence or obstruction. Conclusions: In this retrospective observational study, while SBRT was associated with lower costs, there was a greater rate of urinary obstructive toxicity for patients undergoing SBRT compared to IMRT at all time points studied. Whether this increased rate of complication is offset by a higher cure rate or lower cost should be the subject of further study.