A comprehensive quality assurance (QA) device cum program was developed for the commissioning and routine testing of the 6D IGRT systems. In this article, both the new QA system and the BrainLAB IGRT system which was added onto a Varian Clinac were evaluated. A novel compound 6D-offset simulating phantom was designed and fabricated in the Prince of Wales Hospital (PWH), Hong Kong. The QA program generated random compound 6D-offset values. The 6D phantom was simply set up and shifted accordingly. The BrainLAB ExacTrac X-ray IGRT system detected the offsets and then corrected the phantom position automatically through the robotic couch. Routine QA works facilitated data analyses of the detection errors, the correction errors, and the correlations. Fifty sets of data acquired in 2011 in PWH were thoroughly analyzed. The 6D component detection errors and correction errors of the IGRT system were all within ± 1 mm and ± 1° individually. Translational and rotational scalar resultant errors were found to be 0.50 ± 0.27 mm and 0.54 ± 0.23°, respectively. Most individual component errors were shown to be independent of their original offset values. The system characteristics were locally established. The BrainLAB 6D IGRT system added onto a regular linac is sufficiently precise for stereotactic RT. This new QA methodology is competent to assure the IGRT system overall integrity. Annual grand analyses are recommended to check local system consistency and for external cross comparison. The target expansion policy of 1.5 mm 3D margin from CTV to PTV is confirmed for this IGRT system currently in PWH.