How should we implement disease control programmes so as to strengthen existing health systems? To answer this question, we re-examined the integration of these programmes from a managerial perspective. Based on a literature review, we concluded that integration is essential in the majority of cases. We went on to examine the mechanisms whereby the integration of disease control activities can jeopardize health care delivery, resulting in low service utilization, low detection and cure rates, and patient delays. To do this we clustered disease control programmes into three categories and assessed the impact of each on local health care facilities. From these results, we suggest a series of measures designed to help aid agencies and national governments support local health care infrastructures or, as a minimum, avoid damaging them. Whilst some vertical programmes should never be integrated, two conditions are essential to the integration of others: (1) Disease control needs to be integrated with general health care delivery--which implies the possibility to deliver general practice/family medicine care in publicly oriented health services. (2) Integration of both operational and administrative aspects should take place simultaneously. Any health policies in developing countries tending to allocate disease control programmes to government facilities and general health care to private facilities preclude their integration. They risk unravelling the fabric on which both disease control and health care delivery depend.