Background: MRI has several advantages relative to other imaging modalities in evaluating, diagnosing, and planning treatment for prostate cancer yet it is rarely ordered for localized disease. While the diagnostic abilities have been studied, little has been done to associate clinical outcomes with prostate cancer patients who received MRI. We evaluated the effect of pre-treatment MRI on genitourinary (GU) and gastrointestinal (GI) toxicity in prostate cancer patients who received definitive radiation treatment. Methods: We retrospectively analyzed prostate cancer patients who underwent definitive radiation treatment at our facility between January 01, 1999 and July 31, 2014. All patients who underwent MRI of the pelvis or prostate within 5 years prior to treatment were included in the MRI cohort. The American Urological Symptom Score (AUA) and Rectal Assessment Scale (RAS) were used to measure GU and GI toxicity, respectively. We compared the toxicity profile of patients in our MRI cohort to a comparable cohort of patients who did not receive pre-treatment MRI. Results: 1085 patients (211 with MRI) were analyzed. Median follow-up was 30 months. Mean increase from baseline in AUA scores at 6 months was 3.58 for the MRI cohort and 5.04 for the comparison cohort (p = 0.017). RAS scores were not significantly different between the MRI and comparison cohorts at 6 months (mean increase: 0.62 vs. 0.77, p = 0.662). AUA scores returned to baseline after 6 months in the MRI cohort and after 12 months in the comparison cohort. RAS scores returned to baseline after 12 months in the MRI cohort but never returned to baseline in the comparison cohort. Biochemical failure rates were not significantly different between the MRI cohort and comparison cohort (86.3% vs. 91.1%, p = 0.083). Conclusions: Pre-treatment MRI was associated with significantly less GU and GI toxicity. These results may be influenced by more advanced disease and higher use of hormonal therapy in the MRI cohort. Future prospective studies in a risk-matched cohort are required to validate these findings.