The purpose of this study is to incorporate the dosimetric effect of random patient positioning uncertainties directly into a commercial treatment planning system's IMRT plan optimization algorithm through probabilistic treatment planning (PTP) and compare coverage of this method with margin-based planning. In this work, PTP eliminates explicit margins and optimizes directly on the estimated integral treatment dose to determine optimal patient dose in the presence of setup uncertainties. Twenty-eight prostate patient plans adhering to the RTOG-0126 criteria are optimized using both margin-based and PTP methods. Only random errors are considered. For margin-based plans, the planning target volume is created by expanding the clinical target volume (CTV) by 2.1 mm to accommodate the simulated 3 mm random setup uncertainty. Random setup uncertainties are incorporated into IMRT dose evaluation by convolving each beam's incident fluence with a sigma = 3 mm Gaussian prior to dose calculation. PTP optimization uses the convolved fluence to estimate dose to ensure CTV coverage during plan optimization. PTP-based plans are compared to margin-based plans with equal CTV coverage in the presence of setup errors based on dose-volume metrics. The sensitivity of the optimized plans to patient-specific setup uncertainty variations is assessed by evaluating dose metrics for dose distributions corresponding to halving and doubling of the random setup uncertainty used in the optimization. Margin-based and PTP-based plans show similar target coverage. A physician review shows that PTP is preferred for 21 patients, margin-based plans are preferred in 2 patients, no preference is expressed for 1 patient, and both autogenerated plans are rejected for 4 patients. For the PTP-based plans, the average CTV receiving the prescription dose decreases by 0.5%, while the mean dose to the CTV increases by 0.7%. The CTV tumor control probability (TCP) is the same for both methods with the exception of one case in which PTP gave a slightly higher TCP. For critical structures that do not meet the optimization criteria, PTP shows a decrease in the volume receiving the maximum specified dose. PTP reduces local normal tissue volumes receiving the maximum dose on average by 48%. PTP results in lower mean dose to all critical structures for all plans. PTP results in a 2.5% increase in the probability of uncomplicated control (P+), along with a 1.9% reduction in rectum normal tissue complication probability (NTCP), and a 0.7% reduction in bladder NTCP. PTP-based plans show improved conformality as compared with margin-based plans with an average PTP-based dosimetric margin at 7100 cGy of 0.65 cm compared with the margin-based 0.90 cm and a PTP-based dosimetric margin at 3960 cGy of 1.60 cm compared with the margin-based 1.90 cm. PTP-based plans show similar sensitivity to variations of the uncertainty during treatment from the uncertainty used in planning as compared to margin-based plans. For equal target coverage, when compared to margin-based plans, PTP results in equal or lower doses to normal structures. PTP results in more conformal plans than margin-based plans and shows similar sensitivity to variations in uncertainty.