Background: Despite advances in multimodality treatment of head and neck squamous cell carcinoma (HNSCC), survival outcomes have improved minimally. This may be attributable to the increased risk of secondary primary malignancies. We conducted a retrospective analysis of patients treated at Fremantle Hospital, Western Australia with HNSCC to investigate the incidence of second primary malignancy (SPM), the epidemiological risk factors and survival outcome. Methods: We analyzed 790 patients from our departmental head and neck oncology database with the diagnosis of synchronous and/or metachronous HNSCCs between 1993 and 2011. We analyzed for an association between the risk factors and survival outcomes using the Statistical Package for Social Sciences for statistical analysis. Results: The commonest HNSCC was lip and oral cavity (37.8%), followed by oropharynx (28.1%) and larynx (26.5%). Of the 790 patients, 55.9% were smokers, 36.8% had a smoking history of over 50 pack-years, and 41.1% had a history of alcohol use. Primary treatment included surgery, surgery/ radiotherapy, chemotherapy, surgery/chemotherapy, surgery/chemo-radiotherapy, radiotherapy, chemoradiotherapy, and palliative, or no treatment. Synchronous tumour occurred in 29 patients (3.7%). Eighteen patients (2.3%) had metachronous tumour: median follow-up period was 25 months; 178 patients (22.5%) were dead at the end of follow-up. Conclusions: While this study found a lower rate of secondary primary malignancies in patients with HNSCCs than other studies, there was a clear association between patients with significant smoking histories and the development of HNSCCs. Progression to synchronous or metachronous malignancy was associated with a poorer overall survival rate.