Background Non-communicable diseases (NCD) accounts for more than a third (37%) of all deaths in South Africa. However, this burden of disease can be reduced by addressing risk factors. The aim of this study was to determine the health and risk profile of South African employees presenting for health risk assessments and to measure their readiness to change and improve lifestyle behaviour. Methods Employees (n = 1954) from 18 companies were invited to take part in a wellness day, which included a health-risk assessment. Self-reported health behaviour and health status was recorded. Clinical measures included cholesterol finger-prick test, blood pressure and Body Mass Index (BMI). Health-related age was calculated using an algorithm incorporating the relative risk for all case mortality associated with smoking, physical activity, fruit and vegetable intake, BMI and cholesterol. Medical claims data were obtained from the health insurer. Results The mean percentage of participation was 26% (n = 1954) and ranged from 4% in transport to 81% in the consulting sector. Health-related age (38.5 ± 12.9 years) was significantly higher than chronological age (34.9 ± 10.3 yrs) (p < 0.001). Both chronological and risk-related age were significantly different between the sectors (P < 0.001), with the manufacturing sector being the oldest and finance having the youngest employees. Health-related age was significantly associated with number of days adversely affected by mental and physical health, days away from work and total annual medical costs (p < 0.001). Employees had higher rates of overweight, smoking among men, and physical inactivity (total sample) when compared the general SA population. Increased health-related expenditure was associated with increased number of risk factors, absenteeism and reduced physical activity. Conclusion SA employees' health and lifestyle habits are placing them at increased risk for NCD's, suggesting that they may develop NCD's earlier than expected. Inter-sectoral differences for health-related age might provide insight into those companies which have the greatest need for interventions, and may also assist in predicting future medical expenditure. This study underscores the importance of determining the health and risk status of employees which could assist in identifying the appropriate interventions to reduce the risk of NCD's among employees.