Background: Head and neck (HN) cancer treatment response relies heavily on macroscopic clinical findings. Monitoring of circulating markers during treatment may improve detection of responders versus non-responders during radiotherapy (RT). Our work prospectively describes the changes in gross tumor volume (GTV), circulating tumor cell (CTC), and cell-free DNA (cfDNA) enumeration during RT. Methods: Patients with intact HN squamous cell carcinoma were enrolled in a prospective IRB-approved study. Pre-, after first RT, weekly in-, and post-RT blood samples were collected. Serial pre-, weekly in-, and post-RT magnetic resonance imaging (MRI) was obtained. Serial GTV measurements were recorded. CTC was enumerated using the FDA-approved CellSearch (Menarini Silicon Biosystems) system. Plasma were collected and cfNA from pre-, mid- and post-RT timepoints were isolated using the MagMAX Nucleic Acid Isolation Kit (Thermo Fisher Scientific), and cfDNA were quantified with Qubit high sensitivity dsDNA assay (Invitrogen). Results: 40 patients were eligible for analysis. Median age was 60 years and 36 were males. The median pre-RT GTV was 14.1cc (range 1.3 – 44.9cc). There was a median reduction of 81% in GTV by week 4 (p < 0.0001). Of the 341 samples analyzed for CTC, 146 (43%) had detectable CTC. 7 patients had detectable pre-RT CTCs (1-3/7.5ml blood). There was no correlation between cancer stage, nodal status, and GTV with detection of CTC. After 1 fraction of RT, 14 patients had CTCs detected, including 11 who had no CTC detected prior. All patients had CTC detected at some point during RT except for 2 patients who had none. In week 4, with significant reduction in GTV, 25 (63%) had detectable CTC. 16 and 11 patients had detectable CTC in final week and post-RT timepoints. The cfDNA levels increased during RT, with its highest level in the final week of RT and lowest at post-RT time-point, inversely correlated with GTV. Conclusions: Our study showed that CTCs can be detected during RT, suggesting mobilization into peripheral circulation during RT with unknown viability. cfDNA kinetics during RT correlated with CTC release, and may indicate apoptotic change during RT. Combined cfDNA-CTC as an early marker of treatment response should be investigated further.