Purpose: The feasibility of total marrow irradiation (TMI) using highly conformal image‐guided Tomotherapy is recently being explored as a radiation dose escalation pre‐conditioning TMI regimen for high risk hematological malignancies. Though, initial trial shows potential of this technology, treatment procedure is at present an open loop. This is a concern for safety as well as accuracy of the treatment delivery. The primary objective of this study is to develop a real time optical tracking system (OTS) which will offer better understanding of intra‐fraction whole body motion and develop a closed loop feedback approach to treatment that will enhance the safety of this new treatment. Method and Materials: A stereoscopic camera system is utilized to track near‐infrared reflective markers placed on the Rando phantom. The cameras were calibrated to determine the 3D location of each detected marker. The entire stereoscopic marker detection system returns a set of 3D marker locations at a rate of 60 Hz. Five criteria for evaluating motion capture technology are considered for selection of the optical detection system — accuracy, bandwidth, frame rate, capture volume, and real time performance. The translational motion detection uncertainties in OTS are measured and compared with onboard three dimensional megavoltage CT (MVCT) scanning system for pre‐treatment setup verification. Results: The preliminary work has shown : (i) the translational motion with better than 4mm accuracy, (ii) the vision‐based acquisition can be performed very quickly (in second) compared to the MVCT scan (5–10 minutes) method currently used for initial patient positioning; (iii) bony portions of the body can be accurately tracked in three dimensions. Conclusion: The proposed method entices the effectiveness of vision‐based whole body patient motion tracking for use with the helical tomotherapy treatment.