We evaluated the ability of a commercial respiratory gating system to assure the reproducibility of internal anatomy in respiration synchronized CT (RS-CT) scans. This passive system uses an infrared sensitive camera to track the motion of reflective markers mounted on the abdomen. Eighteen patients, nine with lung tumors and nine with liver tumors, were selected for evaluation of the Varian Real-Time Position Monitor respiratory gating system. Liver tumors were chosen as surrogate for lower lobe tumors. Each patient underwent at least two identical RS-CT scans, at end-inspiration (EI) or end-expiration (EE), to assess intra-fraction reproducibility. Twelve patients also underwent a free breathing scan and an opposed-respiration phase synchronized scan (EI if the two first were an EE and vice versa). On each CT, a physician contoured the liver, the kidneys, the spleen, and the diaphragms for the liver patients; and similarly, the lungs, the gross tumor volume (GTV), the trachea, the heart and the diaphragms for the lung patients. After registering the different CT images using bony anatomy, the changes of each structure between the respective data sets were quantified in terms of its volume, the displacement of its center of mass (COM), and an "index" coefficient of reproducibility. An analysis of the CT scans obtained at EI and EE phases yielded an average superior-inferior (SI) difference of the diaphragm position of 14.4 mm (range: 45.9-0.9). A similar analysis of CT scans acquired at the same breathing phase yielded 0.7 mm (range: 3.1-0, p=0.0001). Similar conclusions were derived in analysis of COM positions of the following structures: lungs, heart, lung's GTV, liver, spleen and kidneys. Evaluation of volume changes for lungs, liver, and spleen confirmed reproducibility of RS-CT while the "index" coefficient confirmed reproducibility of RS-CT of all organs. A commercial gating system using external markers for RS-CT significantly improves the positional reproducibility of thoracic and upper abdominal structures. This reproducible decrease in organ motion will allow a reduction of the margin of expansion facilitating increase in target dose beyond that allowed by conventional radiation treatments.