To evaluate the incidence of a subsequent primary thyroid malignancy in patients with an index head and neck squamous cell carcinoma (HNSCC), we analyzed the National Cancer Institute's Surveillance, Epidemiology, and End Results database to identify a cohort of patients who had been diagnosed with a primary HNSCC from 1973 through 2004. The study population was made up of 60,323 patients of all ages, roughly three-quarters of whom were male. A total of 60 patients (0.1%) developed a subsequent thyroid malignancy-not a statistically significant finding. The overall standard incidence ratio (SIR) for a subsequent thyroid malignancy was 1.58 (p < 0.05). The highest SIRs were seen during in the first 5 years after diagnosis of the original primary (SIR: 3.05; p < 0.05), more specifically in 2 to 11 months after diagnosis (SIR: 7.11; p < 0.05). Further analyses demonstrated that SIRs were significantly higher in males (SIR: 1.71), in patients aged 60 through 79 years (SIR: 1.71), in whites (SIR: 1.55), in patients who had undergone external-beam radiotherapy for their index primary (SIR: 1.84), in those whose tumor was initially staged as regional (SIR: 1.96), and in patients whose index primary was in the oral cavity (SIR: 1.71) or larynx (SIR: 1.88) (p < 0.05 for all). We conclude that the incidence of a subsequent primary thyroid malignancy in patients with an HNSCC is highest during the first 5 years after diagnosis of the index primary, reflecting the benefit of continued surveillance.