Abstract Background The loss of human resource capacity has had a severe impact on the health system in South Africa. This study investigates the causes of migration focussing on the role of salaries and benefits. Health professionals from public, private and non-governmental (NGO) health facilities located in selected peri–urban and urban areas in KwaZulu-Natal, South Africa were surveyed about their current positions and attitudes toward migration. Methods The study uses cross-sectional data collected in 2009. A total of 694 health professionals (430 in the public sector, 133 in the NGO sector and 131 in the private sector) were surveyed. An additional 11 health professionals were purposively selected for in-depth interviews. Odds ratios with 95% confidence intervals were calculated to determine whether salaries influenced HWs decisions to migrate. Results HWs decision to move was not positively associated with lower salaries. It was found, instead, that the consideration to move was determined by other factors including age, levels of stress experienced and the extent to which they were satisfied at their current place of work. Conclusions The OSD appears to have lowered the risk of HWs migrating due to low salaries. However, the results also indicate that the South African Department of Health needs to improve working conditions for HWs within the public health sector to assist in retention.