Objective To characterize the causes of mortality and standardised mortality ratio in a cohort of patients with systemic sclerosis (SSc). Methods A cohort of 132 patients enrolled at the Waikato Systemic Sclerosis Clinic was prospectively followed from 2005 to 2016. Patient demographics, diagnoses and laboratory reports were used to assess risk of mortality and generate standardised mortality ratios (SMR). Survival was analyzed using Kaplan-Meier methods. Results Of the cohort of 132 patients, 20 (15%) were deceased by the end of the study period. The median age of diagnosis and death was 52 years (range 13–86) and 71 years (range 42–87) respectively. Seventy percent of deaths were SSc related and the leading causes of death were due to pulmonary arterial hypertension (PAH), interstitial lung disease (ILD) and scleroderma renal crisis (SRC). Patients diagnosed after the age of 60 had renal or cardiac manifestations and were associated with a significantly increased risk of mortality. The overall SMR was 2.59 (95% CI 1.67–4.01) and was higher in those with diffuse versus limited SSc (6.46, 95% CI 3.08–13.54 vs. 1.93, 95% CI 1.10–3.41) and males (4.17, 95% CI 1.74–10.02 vs. 2.30, 95% CI 1.39–3.81). Conclusion This study demonstrated an increased risk of mortality in patients with SSc relative to that of the general population. An excess in risk was observed particularly in those with diffuse SSc and in males. Renal and cardiac involvement were found to be significant indicators of mortality and reinforces the necessity of screening for these complications.