The study carries out epidemiological transition analysis of disease burden from 1995 to 2014 in India and States for selected diseases. Disability Adjusted Life Years (DALY) methodology has been adapted for disease burden estimation using Medical Certification of Cause of Death (MCCD) and Sample Registration Survey data. The study further elaborates on the essence of decomposition into age structure, death rate and age at death in order to better analyze health system progression. Results indicate wide diversity among states in bearing the burden of communicable, non-communicable and injury. Some states like Bihar, Chhattisgarh and Madhya Pradesh are facing the dual burden of diseases. Findings of the study would be useful in tailoring health care expenditures at regional level based on population health needs thus improving technical and allocative efficiency of health systems.