To determine the systematic error (∑), random error (σ) and derive PTV margin at different levels of the target volumes in Nasopharyngeal Cancer (NPC). A retrospective offline review was done for patients who underwent IMRT for NPC from June 2015 to May 2016 at our institution. Alternate day kV images were matched with digitally reconstructed radiographs to know the setup errors. All radiographs were matched at three levels - the clivus, third cervical (C3) and sixth cervical (C6) vertebra. The shifts in positions along the vertical, longitudinal and lateral axes were noted and the ∑ and σ at three levels were calculated. PTV margins were derived using van Herk's formula. Twenty patients and 300 pairs of orthogonal portal films were reviewed. The ∑ for the clivus, C3 and C6 along vertical, longitudinal and lateral directions were 1.6 vs. 1.8 vs. 2mm; 1.2 vs. 1.4 vs. 1.4mm and 0.9 vs. 1.6 and 2.3mm, respectively. Similarly, the random errors were 1.1 vs. 1.4 vs. 1.8mm; 1.1 vs. 1.2 vs. 1.2mm and 1.2 vs. 1.3 vs. 1.6mm. The PTV margin at the clivus was 4.4mm along the vertical, 4mm along the longitudinal direction and 3.2m in the lateral direction. At the C3 level, it was 5.5mm in the vertical, 5mm in the lateral direction and 4.4mm in the longitudinal direction. At the C6 level, it was 6.4mm in the vertical, 6.9mm in the lateral direction and 4.4mm in the longitudinal direction. A differential margin along different levels of target may be necessary to adequately cover the target.