This paper presents a population-based retrospective cohort study to identify the differences in secondary primary cancer (SPC) among hypopharyngeal, laryngeal, and other sites of head and neck cancer (HNC). Data were collected from the Taiwan National Health Insurance Research Database (NHIRD) for the period 1979-2010. The study cohort comprised 5914 newly diagnosed hypopharyngeal and laryngeal patients from the registry of the Catastrophic Illness Patients Database (CIPD). The comparison cohort comprised 5914 patients with other sites of HNC. We used a multivariate Cox proportional-hazards regression model to assess the risk of developing SPC. The incidence of SPC in the study cohort was 68% higher compared with the comparison cohort (23.9 vs. 14.2 per 1000 person-years, Incident Rate Ratio = 1.68). The study cohort had a higher adjusted hazard ratio (HR) in oesophageal cancer (HR = 3.47) and lung cancer (HR = 1.89). The difference in SPC incidence between the study and comparison cohort was significant.