Background: Angiogenesis plays an important role in head and neck squamous cell carcinoma (HNSCC) progression. This pilot study was designed to compare the distribution of 68 Ga-NODAGA-RGD PET/CT for imaging α v β 3 integrins involved in tumor angiogenesis to 18 F-FDG PET/CT in patients with HNSCC. Material and methods: Ten patients (aged 58.4 ± 8.3 years [range, 44-73 years], 6 males, 4 females) with a total of 11 HNSCC were prospectively enrolled. Activity mapping and standard uptake values (SUV) from both 68 Ga-NODAGA-RGD and 18 F-FDG PET/CT scans were recorded for primary tumor and compared with the Wilcoxon signed-rank test. The relation between the SUV of both tracers was assessed using the Spearman correlation. Results: All HNSCC tumors were visible with both tracers. Quantitative analysis showed higher 18 F-FDG SUV max in comparison to 68 Ga-NODAGA-RGD (14.0 ± 6.1 versus 3.9 ± 1.1 g/mL, p = 0.0017) and SUV mean (8.2 ± 3.1 versus 2.0 ± 0.8 g/mL, p = 0.0017). Both 18 F-FDG and 68 Ga-NODAGA-RGD uptakes were neither correlated with grade, HPV status nor p16 protein expression (p ≥ 0.17). Conclusion: All HNSCC tumors were detected with both tracers with higher uptake with 18 F-FDG, however. 68 Ga-NODAGA-RGD has a different spatial distribution than 18 F-FDG bringing different tumor information.