Policy initiatives to improve retention of the rural health workforce have relied primarily on evidence for rural doctors, most of whom practice under a private business model. Much of the literature for rural allied health (AH) workforce focuses on the public sector. The AH professions are diverse, with mixed public, private or combined practice settings. This study explores sector differences in factors affecting retention of rural AH professionals. This study compared respondents from the 2008 Rural Allied Health Workforce (RAHW) survey recruiting all AH professionals in rural New South Wales. Comparisons between public (n = 833) and private (n = 756) groups were undertaken using Chi square analysis to measure association for demographics, job satisfaction and intention to leave. The final section of the RAHW survey comprised 33 questions relating to retention. A factor analysis was conducted for each cohort. Factor reliability was assessed and retained factors were included in a binary logistic regression analysis for each cohort predicting intention to leave. Six factors were identified: professional isolation, participation in community, clinical demand, taking time away from work, resources and 'specialist generalist' work. Factors differed slightly between groups. A seventh factor (management) was present only in the public cohort. Gender was not a significant predictor of intention to leave. Age group was the strongest predictor of intention to leave with younger and older groups being significantly more likely to leave than middle aged.In univariate logistic analysis (after adjusting for age group), the ability to get away from work did not predict intention to leave in either group. In multivariate analysis, high clinical demand predicted intention to leave in both the public (OR = 1.40, 95% CI = 1.08, 1.83) and private (OR = 1.61, 95% CI = 1.15, 2.25) cohorts. Professional isolation (OR = 1.39. 95% CI = 1.11, 1.75) and Participation in community (OR = 1.57, 95% CI = 1.13, 2.19) also contributed to the model in the public cohort. This paper demonstrates differences between those working in public versus private sectors and suggests that effectiveness of policy initiatives may be improved through better targeting.