Planning target volume (PTV) to deliver the desired dose to the clinical target volume (CTV) accounts for systematic (∑) and random (σ) errors during the planning and execution of intensity modulated radiation therapy (IMRT). As these errors vary at different departments, this study was conducted to determine the 3-dimensional PTV (PTV3D) margins for head and neck cancer (HNC) at our center. The same was also estimated from reported studies for a comparative assessment. A total of 77 patients with HNCs undergoing IMRT were included. Of these, 39 patients received radical RT and 38 received postoperative IMRT. An extended no action level protocol was implemented using on-board imaging. Shifts in the mediolateral (ML), anteroposterior (AP), and superoinferior (SI) directions of each patient were recorded for every fraction. PTV margins in each direction (ML, AP, SI) and PTV3D were calculated using van Herk's equation. Weighted PTV3D was also computed from the ∑ and σ errors in each direction published in the literature for HNC. Our patients were staged T2-4 (66/77) and N0 (39/77). In all, 2280 on-board images were acquired, and daily shifts in each direction were recorded. The PTV margins in the ML, AP, and SI directions were computed as 3.2 mm, 2.9 mm, and 2.6 mm, respectively. The PTV3D margin was estimated to be 6.5 mm. This compared well with the weighted median PTV3D of 7.2 mm (range: 3.2 to 9.9) computed from the 16 studies reported in the literature. To ensure ≥95% CTV dose coverage in 90% of HNC patients, PTV3D margin for our department was estimated as 6.5 mm. This agrees with the weighted median PTV3D margin of 7.2 mm computed from the 16 published studies in HNCs. Site-specific PTV3D margin estimations should be an integral component of the quality assurance protocol of each department to ensure adequate coverage of dose to CTV during IMRT.