The functions of the Health Protection Agency are to protect against infectious diseases and other public health concerns in the United Kingdom. On April 1st, 2005, HPA was established as an independent agency, replacing the 2003 HPA Special Health Authority and the National Radiological Protection Board (NRPB) and radiation protection as part of health protection was incorporated in its remit. The National Institute of Biological Standards and Control (NIBSC) merged into the Health Protection Agency on 1 April 2009.

The Agency's role focuses on reducing the dangers to health from infections and chemical and radiation hazards and also preparing for public health emergencies. The Agency provides support to and works in partnership with other organizations that also have health protection responsibilities and provides advice, through the Department of Health, to all government departments and devolved administrations throughout the UK.  In England, it provides the local health protection services which in the rest of the UK are delivered by the three other lead health protection bodies: the National Public Health Service Wales, Health Protection Scotland, and Department of Health, Social Services and Public Safety, Northern Ireland.

The Agency has 3,160 staff members and three main centers: Centre for Emergency Preparedness and Response (Porton Down, Salisbury), Centre for Infections (Colindale, North London), and Centre for Radiation, Chemicals and Environmental Hazards (Chilton, Oxon). Major departments also include the National Institute of Biological Standards and Control (South Mimms, Hertfordshire), Regional Microbiology Network, Local and Regional Services, and Corporate Services.

In 2008, the institute played a key role in introducing the HPV vaccine for girls aged 12-13. During the year, agency staff responded to 4,000 local and regional public health incidents and outbreaks, including infectious diseases and chemical and radiation incidents.