AIM: To compare different markers of socioeconomic status (SES) with cardiovascular disease (CVD) and diabetes risk factors. METHODS: Data were from 4020 participants aged 35-74 years from the Diabetes, Heart and Health Survey that was carried out in 2002 and 2003. Measures of SES were the occupation-based NZ Socioeconomic Index (NZSEI), combined household income, education, and the area-based deprivation measure NZDep2001. RESULTS: After adjusting for all other SES measures, there were relatively few independent risk factor associations with NZSEI or education. Both low income and being more deprived as measured by NZDep2001 were independently associated with higher 2-hour glucose tolerance concentrations, HbA1c levels, waist-to-hip ratio, urinary albumin concentrations, 5-year CVD risk, current cigarette smoking, lower HDL-cholesterol, and less time spent exercising compared to the highest SES strata. Low income was independently associated with a higher prevalence of total and previously diagnosed diabetes mellitus, and lower stature. More deprivation was independently associated with higher diastolic blood pressure levels, fasting glucose concentrations and BMI. Associations with height, and 2-hour glucose levels, and prevalence of total and previously diagnosed diabetes were greater with income, whereas NZDep2001 showed stronger associations with diastolic blood pressure, raised blood pressure, HDL-cholesterol, fasting glucose, BMI, waist-to-hip ratio, exercise levels, urinary albumin concentrations, 5-year risk of CVD and prevalence of smoking compared to the highest SES groups. Associations of income and NZDep2001 with HbA1c were similar. CONCLUSIONS: Cardiovascular disease and diabetes risk factors were more strongly associated with the area-based NZDep2001 and household income than with the individual's occupation-based NZSEI or education. In general, the strongest associations were observed for NZDep. These findings provide support for the application of NZDep in health policy development in New Zealand, when other measures of SES are not available, and we recommend that this very accessible indicator of socioeconomic and health status continue to be updated.