Introduction: In intensity modulated radiotherapy (IMRT) of nasopharyngeal carcinoma (NPC) patients, an effective immobilisation system is important to minimise set up deviation. This study evaluated the effectiveness of three immobilisation systems by assessing their set up deviations. Methods: Patients were randomly assigned to one of the three immobilisation systems: (1) supine on head rest and base plate (HB); (2) supine with alpha cradle supporting the head and shoulder (AC); (3) supine with vacuum bag supporting the head and shoulder (VB). CBCT was conducted weekly for each patient on the linear accelerator. Image registration was conducted at the nasopharynx (NP) and cervical regions. The translational displacements (latero-medial, anteroposterior and cranio-caudal), rotational displacements (pitch, yaw and roll) and 3D vectors obtained at the NP and cervical regions were recorded and compared among the three systems. Results: The mean translational and rotational deviations were within 3 mm and 2 degrees, respectively, and the range of 3D vector was 1.53-3.47 mm. At the NP region, the AC system demonstrated the smallest translational and rotational deviations and 3D vector. The differences were significant except for the latero-medial, yaw and roll directions. Similarly, at the cervical region, the AC system showed smaller translational and rotational deviations and 3D vector, with only the cranio-caudal and yaw deviations that did not reach statistical significance. Conclusions: Set up deviation was greater in the neck than the NP region. The set up accuracy of the AC system was better than the other two systems, and it is recommended for IMRT of NPC patients in our institution.