We developed a method to analyze quantitatively the residual cord geometrical uncertainties after image registration during head and neck radiation therapy by using sequential cone beam CT (CBCT). The geometrical centroid line of cervical spinal canal was computed to serve as a cord surrogate. We found that the cord motions were non-uniform from C1 to C6, and that the patterns of motion were variable across patients. This method has potential applications in monitoring cord setup accuracy and in designing treatment margins.