This study examines trends in chronic disease outcomes from initiation of a specialised chronic disease treatment programme through to incorporation of programme activities into routine service delivery. We reviewed clinical records of 98 participants with confirmed renal disease or hypertension in a remote indigenous community health centre in Northern Australia. For each participant the review period spanned an initial three years while participating in a specialised cardiovascular and renal disease treatment programme and a subsequent three years following withdrawal of the treatment programme. Responsibility for care was incorporated into the comprehensive primary care service which had been recently redeveloped to implement best practice care plans. The time series analysis included at least six measures prior to handover of the specialised programme and six following handover. Main outcome measures were trends in blood pressure (BP) control, and systolic and diastolic BP. We found an improvement in BP control in the first 6-12 months of the programme, followed by a steady declining trend. There was no significant difference in this trend between the pre- compared to the post-programme withdrawal period. This finding was consistent for control at levels below 130/80 and 140/90, and for trends in mean systolic and diastolic BP. Investigation of the sustainability of programme outcomes presents major challenges for research design. Sustained success in the management of chronic disease through primary care services requires better understanding of the causal mechanisms related to clinical intervention, the basis upon which they can be 'institutionalised' in a given context, and the extent to which they require regular revitalisation to maintain their effect.