Background In this study we investigate the accuracy of industrial six axes robots employed for patient positioning at the Heidelberg Ion Beam Therapy Center. Methods In total 1018 patient setups were monitored with a laser tracker and subsequently analyzed. The measurements were performed in the two rooms with a fixed horizontal beam line. Both, the 3d translational errors and the rotational errors around the three table axes were determined. Results For the first room the 3d error was smaller than 0.72 mm in 95 percent of all setups. The standard deviation of the rotational errors was at most 0.026° for all axes. For the second room Siemens implemented an improved approach strategy to the final couch positions. The 95 percent quantile of the 3d error could in this room be reduced to 0.53 mm; the standard deviation of the rotational errors was also at most 0.026°. Conclusions Robots are very flexible tools for patient positioning in six degrees of freedom. This study proved that the robots are able to achieve clinically acceptable accuracy in real patient setups, too.