Background: The volume of rectum receiving high-dose (i.e. > or = 60 Gy) is consistently associated with the risk of Grade > or = 2 rectal toxicity or rectal bleeding based on common terminology criteria for adverse events (CTCAE). Our goal was to compare intensity-modulated photon radiotherapy (IMRT) with proton radiotherapy in regard to the rectal dose using the normal tissue complication probability (NTCP). Methods: Between July 2014 and September 2015 the first 10 consecutive low or intermediate risk prostate cancer patients were treated with proton therapy at our institution. All 10 patients were planned with three-dimensional conformal proton therapy (3D-CPT) using two parallel opposed fields as well as comparison IMRT plans. A rectal balloon filled with water was used in all patients treated. Prescribed dose to the prostate was 79.2 Gy or cobalt Gy equivalent (CBE) for protons. Dose-volume histograms were compared. The Lyman-Kutcher-Burman model (n = 0.09, m = 0.13, and TD₅₀ = 76.9 Gy) was used to generate NTCP estimates for both IMRT and proton plans. Results: At least 95% of the planning target volume received the prescription dose for both proton and IMRT plans. Dose constraints placed on the rectum included volume receiving 65 Gy (V₆₅) less than 17% and V₄₀ less than 35%. The mean dose to the rectum was 24.5 Gy (range, 19.5-30.1 Gy) and 31.7 Gy (range, 23.7-39.4 Gy) for the proton and IMRT plans, respectively. The V₆₅ constraint was unachievable in 3 of the proton plans and 3 of the IMRT plans. The mean V₇₀ andV₇₅ for proton plans was 8.4% and 5.4% compared to 7.5% and 4.8% for the IMRT plans. The mean NTCP for proton treatment plans was 7.72% (range, 2.7-11.7%) and 7.92% (range, 1.7-15.3%) for IMRT (P = 0.45). After median follow-up of 6 months, no grade 2 or higher toxicity has been reported. Conclusions: Utilizing NTCP estimations, proton therapy and IMRT have similar predicted rates of rectal toxicity. Currently, a Phase III randomized clinical trial is underway comparing proton therapy and IMRT with regards to rectal toxicity and quality of life.