Background: In 2005, the South African government introduced a voluntary, subsidised health insurance scheme for civil servants. In light of the global emphasis on universal coverage, empirical evidence is needed to understand the relationship between new health financing strategies and health care access thereby improving global understanding of these issues. Objectives: This study analysed coverage of the South African government health insurance scheme, the population groups with low uptake, and the individual-level factors, as well as characteristics of the scheme, that influenced enrolment. Methods: Multi-stage random sampling was used to select 1,329 civil servants from the health and education sectors in four of South Africa's nine provinces. They were interviewed to determine factors associated with enrolment in the scheme. The analysis included both descriptive statistics and multivariate logistic regression. Results: Notwithstanding the availability of a non-contributory option within the insurance scheme and access to privately-provided primary care, a considerable portion of socio-economically vulnerable groups remained uninsured (57.7% of the lowest salary category). Non-insurance was highest among men, black African or coloured ethnic groups, less educated and lower-income employees, and those living in informal-housing. The relatively poor uptake of the contributory and non-contributory insurance options was mostly attributed to insufficient information, perceived administrative challenges of taking up membership, and payment costs. Conclusion: Barriers to enrolment include insufficient information, unaffordability of payments and perceived administrative complexity. Achieving universal coverage requires good physical access to service providers and appropriate benefit options within pre-payment health financing mechanisms.