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The NCDC has its headquarters in Delhi and has eight outstation branches located at Alwar (Rajasthan), Bengaluru (Karnataka), Kozhikode-Calicut (Kerala), Coonoor (Tamil Nadu), Jagdalpur (Chhatisargh), Patna (Bihar), Rajahmundry (Andhra Pradesh) and Varanasi (Uttar Pradesh). There are 14 Technical Centres/Divisions at the headquarters viz. Centre of Epidemiology, Division of Microbiology, Division of Zoonosis, Centre for Medical Entomology & Vector Management (CME&VM), Integrated Disease Surveillance Programme (IDSP), Centre for AIDS & Related Diseases (CARD), Division of Biochemistry & Toxicology, Division of Biotechnology, Division of Parasitic Disease (DPD), Division of Malariology & Coordination (M&C), Centre for Environment & Occupational Health (CE&OH), Centre for Non-Communicable Diseases (CNCD), Statistical Monitoring & Evaluation Centre (SM&EC) and Division of Planning, Budget & Administration (PBA). In each centre/division, there are sections and laboratories dealing with different communicable and non-communicable diseases. The activities of each division are supervised by the officer-in charge supported by medical and non-medical scientists, research officers and other technical and paramedical staff.
The NCDC branches are also equipped and staffed to carry out field studies, training activities and research.