Strengthening good governance and preventing corruption in health care are universal challenges. The Karnataka Lokayukta (KLA), a public complaints agency in Karnataka state (India), was created in 1986 but played a prominent role controlling systemic corruption only after a change of leadership in 2001 with a new Lokayukta (ombudsman) and Vigilance Director for Health (VDH). This case study of the KLA (2001-06) analysed the:Scope and level of poor governance in the health sector; KLA objectives and its strategy; Factors which affected public health sector governance and the operation of the KLA. We used a participatory and opportunistic evaluation design, examined documents about KLA activities, conducted three site visits, two key informant and 44 semi-structured interviews and used a force field model to analyse the governance findings. The Lokayukta and his VDH were both proactive and economically independent with an extended social network, technical expertise in both jurisdiction and health care, and were widely perceived to be acting for the common good. They mobilized media and the public about governance issues which were affected by factors at the individual, organizational and societal levels. Their investigations revealed systemic corruption within the public health sector at all levels as well as in public/private collaborations and the political and justice systems. However, wider contextual issues limited their effectiveness in intervening. The departure of the Lokayukta, upon completing his term, was due to a lack of continued political support for controlling corruption. Governance in the health sector is affected by positive and negative forces. A key positive factor was the combined social, cultural and symbolic capital of the two leaders which empowered them to challenge corrupt behaviour and promote good governance. Although change was possible, it was precarious and requires continuous political support to be sustained.