Modern radiation therapy (RT) of head and neck cancer (HNC) offers precise delivery to the defined targets while maintaining low doses to surrounding critical organs - in part due to the enhanced ability to define the gross tumor volume (GTV) with the additional use of MRI and PET scans. Traditionally, a high dose clinical target volume (CTV) of 5 mm is routinely added to the GTV to ensure proper coverage of microscopic disease. However, HN tumors often respond during RT, which suggests that the microscopic CTV through a significant portion of the treatment is shrinking to < 5 mm and could be reduced. This study intends to quantify the decrease in CTV margin in a series of HNC patients through the course of the treatment. A prospective study in 2009 enrolled advanced HNC patients undergoing curative IMRT (70 Gy in 33 fractions, with or without chemotherapy) to receive a dynamic pre-treatment fluorodeoxyglucose (FDG) PET-CT simulator scan (with mask), which was also repeated during the 2nd-3rd week. Sixty patients with different HNC were evaluated. Two radiation oncologists separately contoured GTVs in the pre- and intra-treatment scans to account for inter-observer variability. Rigid fusion of the planning CT to pre- and intra- treatment PET-CT scans was performed using the image fusion module. Margin expansions ranging from 1-25 mm were performed on the pre-treatment GTV to volumetrically match the original clinical target volume (CTV) (as defined by the treating radiation oncologist), based on optimal Dice Similarity Indices (DSI). A similar process took place with the intra-treatment scan, where the intra-treatment GTV was expanded to the original treatment CTV. Results from 16 patients are reported with the full patient cohort to follow. Volume matching given by DSI showed that the pre-treatment GTV needed an average 3.12 ± 1.36 mm expansion to optimally match the clinical CTV (DSI = 0.78 ± 0.04) while the 2nd-3rd week GTV required a margin of 5.65 ± 2.03 mm (DSI = 0.70 ± 0.06). On average, the radial size of the primary CTV decreased by 2.53 ± 2.44 mm between pre- and 2nd-3rd week scans. Our results indicate that HNC tumor shrinkage during RT provides an inherent margin that may allow for an overall smaller GTV to CTV expansion. The determination of an optimized CTV margin could permit dose escalation in HNC patients while minimizing normal tissue toxicities.