Operational research, within the context of a national disease control programme, may be described as the search for knowledge on interventions, tools or strategies which enhance programme effectiveness. There are two examples from Malawi of how operational research into recurrent tuberculosis and decentralization of treatment lead to information which enabled the National TB Control Programme (NTP) to change and improve its practice and policy. The key factors which allowed this to happen, and the guiding principles about integrating research into national programmes are discussed. TB programmes must have clear objectives, be able to identify constraints which prevent objectives being met and ask research questions around these constraints. There must be sufficient resources for research, both material and financial, and this requires programmes to incorporate a research agenda into their costed annual workplans. Training is also a key component of developing an integrated research programme, and should be included in the budgets. Research outputs should be judged in terms of activities undertaken and completed, papers written, and regular documentation of how research has influenced policy and practice. Finally, there should be strong advocacy for operational research, so that government policy makers can be convinced of its value.