India is going through a period of transition, both epidemiological and demographic transition. Infectious diseases are still persisting as major health problems in spite of having national programmes for the control of most of these diseases for almost half a century now. This paper focuses on two national programmes: the success story of the National Leprosy Eradication Programme; and the National Anti-Malaria Programme that has failed to achieve its objectives. There are re-emerging infectious diseases which are adding to the burden of diseases. In addition, there is an increasing prevalence of non-communicable diseases as a result of lifestyle changes and urbanization. These are the challenges that are to be tackled in the new millennium.