The term Autonomy implies self ruling, freedom from coercion. In the Kantian tradition, autonomy implies freely embracing a moral obligation, people should be treated as ends in themselves and not as means to an end. Implies two distinct moral requirements: acknowledge autonomy and protect those with diminished autonomy.
In public health/community health autonomy refers to underlying obligation for informed consent in research and decisions regarding study design and interventions.
Source: Weed, D.L., McKeown, R.E., Ethics in epidemiology and public health I. Technical terms, Journal of Epidemiology and Community Health. 2001:55(12): 855–857