The consequences of health sector reforms on control of malaria were analysed using Colombia as an example. One of the most complex health sector reform programmes in Latin America took place in the 1990s; it included transferring the vertical vector-borne disease control (VBDC) programme into health systems at state and district levels. A series of studies was undertaken in 1998-2000 at the national level (Ministry of Health Study), at the state level (Departamento Study) and at the health district level (District Study) using formal and informal interviews among control staff and document analysis as data collection tools. A government-financed national training programme for VBDC staff - which included direct observation of control operations - was also used to analyse health workers' performance in the postreform period (longitudinal study). The results showed that some shortcomings of the old vertical system, such as the negative aspects of trade union activity, have not been overcome while some positive aspects of the old system, such as capacity building, operational planning and supervision have been lost. This has contributed to a decrease in control activity which, in turn, has been associated with more malaria cases. Malaria control had to be reinvented at a much larger scale than anticipated by the reformers caused by a whole series of problems: complex financing of public health interventions in the new system, massive staff reductions, the difficulty of gaining access to district and state budgets, redefining entire organizations and - in addition to the reforms - introducing alternative strategies based on insecticide-treated materials and the growth of areas of general insecurity in many parts of Colombia itself. However, positive signs in the transformed system include: the strengthening of central control staff (albeit insufficient in numbers) when transferred from the Ministry of Health to the National Institute of Health, the opportunities offered by the Basic Health Plan (PAB) for new planning initiatives and intersectoral co-operation and the integration of malaria diagnosis and treatment into the general health services (associated with a decrease of malaria mortality). The potentials of the new system have not yet been fully exploited: capacity building, communication and management skills need to be improved and it require guidance from the national level.