Background: Proton radiotherapy (PRT) is a costly treatment used for prostate cancer despite little evidence supporting its use. We examined patterns of PRT use in the Medicare program and assessed the short-term toxicity of PRT vs. intensity modulated radiation therapy (IMRT). Methods: Using national Medicare claims from 2008-2009, we identified a sample of prostate cancer patients ages 66-94 who had received PRT or IMRT. We used multivariable logistic regression to identify patient and regional factors associated with receipt of PRT. We searched claims for procedure and diagnosis codes indicative of treatment-related complications and grouped the complications into genitourinary (GU), gastrointestinal (GI), and other complications. To compare the effect of PRT and IMRT on short-term toxicity, we used a Mahalanobis distance approach to match each PRT patient to two IMRT patients, achieving balanced distribution of clinical and sociodemographic characteristics. We compared six-month and one-year outcomes between the two treatment groups using conditional logistic regression. Results: We identified 27,647 men; 421 (2%) received PRT and 27,226 (98%) received IMRT. Patients who received PRT were widely geographically distributed, with some patients traveling >500 miles for treatment. PRT patients were younger, healthier, and of higher socioeconomic status. Although PRT was associated with a significant reduction in GU complications at six-months compared with IMRT (6.1% vs. 12.0%, OR 0.60 [95% CI 0.38-0.96], p=0.03), at one-year post-treatment there was no longer any difference in cumulative complication rates (18.9% vs. 21.9%, OR 0.96 [95% CI 0.61-1.53], p=0.88). There was no significant difference in GI or other complications at six-months or one-year post-treatment. Conclusions: Although PRT remains a scarcely used treatment, some prostate cancer patients traveled great distances for treatment. While PRT was associated with a reduction in six-month GU toxicity, there were no differences in toxicity at one-year. Further study on longer-term effects and other clinical and patient-reported outcomes is needed to inform the widespread application of PRT.