Setting: Twenty government departments in Rarotonga, Cook Islands. Objective: To determine the characteristics, presence of selected non-communicable disease (NCD) risk factors and prevalence of diabetes mellitus (DM) and hypertension among government workers who participated in ‘wellness checks’ in 2012. Design: Cross-sectional study involving analysis of survey data. Results: Of 598 employees, 70% were aged 25–54 years and 55% were female. Two thirds were obese (body mass index ?30 kg/m2), and 76% had low levels of fruit and vegetable consumption. Of 50 (8.4%) participants diagnosed with DM (random blood glucose ?11 mmol/l, fasting ?7 mmol/l), 30 were self-reported and 20 were based on blood glucose. Of the 206 (34.4%) diagnosed with hypertension (systolic ?140 and/or diastolic ?90), 71 were self-reported and 135 were based on blood pressure measurements. Obesity was associated with hypertension (OR 2.79, 95%CI 1.4–5.4), but not with DM. No relationship was observed between fruit and vegetable consumption and presence or absence of DM or hypertension. Conclusion: This study identified a high prevalence of obesity and hypertension among government employees in the Cook Islands, risk factors that are associated with NCDs such as DM and cardiovascular disease. ‘Wellness checks’ pave the way for interventions in workplace settings to prevent and better manage these diseases through early diagnosis, risk management, treatment and supportive public health policies.