Job satisfaction is an important determinant of health worker motivation, retention, and performance, all of which are critical to improving the functioning of health systems in low- and middle-income countries. A number of small-scale surveys have measured the job satisfaction and intention to leave of individual health worker cadres in different settings, but there are few multi-country and multi-cadre comparative studies. The objective of this study was to compare the job satisfaction and intention to leave of different categories of health workers in Tanzania, Malawi, and South Africa. We undertook a cross-sectional survey of a stratified cluster sample of 2,220 health workers, 564 from Tanzania, 939 from Malawi, and 717 from South Africa. Participants completed a self-administered questionnaire, which included demographic information, a 10-item job satisfaction scale, and one question on intention to leave. Multiple regression was used to identify significant predictors of job satisfaction and intention to leave. There were statistically significant differences in job satisfaction and intention to leave between the three countries. Approximately 52.1% of health workers in South Africa were satisfied with their jobs compared to 71% from Malawi and 82.6% from Tanzania (χ(2)=140.3, p<0.001). 18.8% of health workers in Tanzania and 26.5% in Malawi indicated that they were actively seeking employment elsewhere, compared to 41.4% in South Africa (χ(2)=83.5, p<0.001). The country differences were confirmed by multiple regression. The study also confirmed that job satisfaction is statistically related to intention to leave. We have shown differences in the levels of job satisfaction and intention to leave between different groups of health workers from Tanzania, Malawi, and South Africa. Our results caution against generalising about the effectiveness of interventions in different contexts and highlight the need for less standardised and more targeted HRH strategies than has been practised to date.