The present study aimed to investigate the clinical relevance of circulating tumor cells (CTCs) in patients with locally advanced head and neck squamous cell carcinoma (LA-HNSCC), particularly in patients with nasopharyngeal and hypopharyngeal squamous cell carcinoma. CTCs were isolated using negative immunomagnetic bead enrichment and were identified by fluorescence in situ hybridization. Youden's index and the receiver operating characteristic (ROC) curve were used to select the optimal CTC baseline value. χ 2 test or Fisher's test were used to determine the association between CTC counts and clinical parameters, curative effects and prognosis. The Kaplan-Meier estimator was used to analyze overall survival (OS) and progression-free survival (PFS). In the present study, 356 peripheral blood samples (178 pretreatment samples and 178 post-treatment samples) from 178 patients were examined. The results revealed that the pretreatment CTC detection rate was 73.8%. The minimum, maximum and median CTC counts were 1, 22 and 2/3.2 ml, respectively. The number of polyploid CTCs was associated with distant metastasis (P=0.026). In addition, patients with undetectable CTCs, and decreasing or negative CTCs post-treatment tended to have a good prognosis (P<0.05). For nasopharyngeal squamous cell carcinoma, the PFS of patients with increased CTCs and CTCs ≥2/3.2 ml after treatment was significantly lower (P<0.05). For hypopharyngeal squamous cell carcinoma, it was suggested that CTCs with a cutoff value of 3 may be used to evaluate PFS and OS before and after treatment. In conclusion, CTCs may be used to monitor disease progression and the response to chemoradiotherapy for patients with LA-HNSCC. Furthermore, CTCs are a better predictor of the prognosis of hypopharyngeal squamous cell carcinoma than that of nasopharyngeal squamous cell carcinoma.