In planning operations for patients with cardiovascular disease, vascular surgeons rely on their training, past experiences with patients with similar conditions, and diagnostic imaging data. However, variability in patient anatomy and physiology makes it difficult to quantitatively predict the surgical outcome for a specific patient a priori. We have developed a simulation-based medical planning system that utilizes three-dimensional finite-element analysis methods and patient-specific anatomic and physiologic information to predict changes in blood flow resulting from surgical bypass procedures. In order to apply these computational methods, they must be validated against direct experimental measurements. In this study, we compared in vivo flow measurements obtained using magnetic resonance imaging techniques to calculated flow values predicted using our analysis methods in thoraco-thoraco aortic bypass procedures in eight pigs. Predicted average flow rates and flow rate waveforms were compared for two locations. The predicted and measured waveforms had similar shapes and amplitudes, while flow distribution predictions were within 10.6% of the experimental data. The average absolute difference in the bypass-to-inlet blood flow ratio was 5.4 +/- 2.8%. For the aorta-to-inlet blood flow ratio, the average absolute difference was 6.0 +/- 3.3%.