Purpose: The current prescription and the assessment of the delivered absorbed dose in intraoperative radiation therapy (IORT) with the INTRABEAM system rely mainly on depth-dose measurements in water. The accuracy of this approach is limited because tissue heterogeneity is ignored. It is also difficult to accurately determine the dose delivered to the patient experimentally as the steep dose gradient is highly sensitive to geometric errors. Our goal is to determine the dose to the target volume and the organs at risk of a clinical breast cancer patient from treatment with the system. Methods: A homogeneous water-equivalent CT dataset was derived from the preoperative CT scan of a patient by setting all materials in the patient volume as water-equivalent. This homogeneous CT data represents the current assumption of a homogenous patient, while the original CT data is considered the ground truth. An in-house Monte Carlo algorithm was used to simulate the delivered dose in both setups for a prescribed treatment dose of 20 Gy to the surface of the 3.5-cm-diameter spherical applicator. Results: The doses received by 2% (D2%) of the target volume for the homogeneous and heterogeneous geometries are 16.26 Gy and 9.33 Gy, respectively. The D2% for the heart are 0.035 Gy and 0.119 Gy for the homogeneous and heterogeneous geometries, respectively. This trend is also observed for the other organs at risk. Conclusions: The assumption of a homogeneous patient overestimates the dose to the target volume and underestimates the doses to the organs at risk.