The CDRI's inhouse research programmes are directed at national health problems and family welfare needs and internationally important disease areas related to changing life style and demography.

The focus of the Institute is research activity is mainly on discovery and development of women healthcare and contraceptive agents, and new drugs for tropical infections (viral, bacterial and parasitic), cardio-vascular and central nervous system disorders in particular those related to ageing , associated memory disorders, and metabolic changes, using leads from traditional knowledge as well as the newer approaches of drug development. Besides, the Institute is also involved in the development of process technologies for generic drugs, intermediates and fermentation products required for the country's healthcare programme.

The drug discovery programme covers development of new drugs from synthetic routes as well as natural sources, which include terrestrial plants and marine flora and fauna. A systematic search of plants described in Ayurveda offers an opportunity to identify the novel "new leads" for the development of modern plant based drugs and herbal remedies. The natural product programme primarily aims at the development of drugs for the treatment of filariasis, Kala-azar, liver damage and diabetic wounds.

Basic research, an essential component of the overall research programme, aims at the generation of new knowledge or new leads, necessary for the success of new drug research programme. Institute's most research projects have a built in basic research component, which is directed towards new drug targets, mode of action studies on candidate drugs, host parasite interactions and the underlying disease mechanism.

To compete in the international markets, CDRI has introduced modern approaches to the drug research covering identification of the novel biological leads and molecular targets, development of in vitro test screens, combinatiorial chemical synthesis, high throughput screening (HTS), genomics, structural biology, molecular modelling in line with the international standards.