Controlling disease in farm animals

How to prevent infections through biosecurity measures, quarantine procedures and what to do if disease breaks out on your farm.


Disease outbreaks among farm animals can cause significant economic damage. However, you can limit the impact through preventative and control measures.

You must ensure that you follow biosecurity procedures, such as cleaning and disinfecting premises and vehicles. If there is an outbreak, government contingency plans will be followed. These plans include designating affected premises, setting up protection and surveillance zones, and controls on livestock movements.

This guide explains the special measures which apply in cases affecting poultry - such as avian influenza or ‘bird flu’ - and to the treatment of fresh meat, milk and milk products in affected areas.

This guide also outlines ways to reduce the risk of animal diseases being transmitted to humans, including procedures to protect visitors on open farms.

For contact details of your local Animal Health and Veterinary Laboratories Agency (AHVLA) use the postcode search tool on the AHVLA website.

Biosecurity and disease control

Biosecurity measures can help prevent the spread of farmed diseases - including notifiable diseases - across the UK. They also protect agricultural workers and visitors. Different biosecurity procedures apply to animals on farms and to animals being moved, for example to markets and agricultural shows.

Disease control through biosecurity focuses on controlling and reducing movements of animals, people and vehicles to and from areas where livestock is kept.

On-farm biosecurity measures include:

  • cleaning and disinfecting protective clothing and vehicles before and after contact with animals
  • use of disposable protective clothing

During an outbreak, the Department for Environment, Food and Rural Affairs (Defra) will usually impose restrictions on animal movements, and suspend agricultural markets and shows. Standard biosecurity measures at markets and shows are based on the ‘clean in, clean off’ principle, for examples:

  • banning vehicles, equipment and clothing contaminated with animal excreta - except vehicle interiors and protective clothing taken off site for laundering
  • cleaning contamination from clothes before leaving animal areas
  • cleaning and disinfecting boots before leaving animal areas

You should check the health status of livestock before buying or selling animals. New animals should be kept separate from existing stock on first arrival.

Read about routine good hygiene and biosecurity measures in the guide on disease prevention.

Biosecurity for specific livestock species

There are also some biosecurity measures that you need to be aware of for specific animals.


Cattle biosecurity measures follow general principles of controlling stock movement, and disinfecting vehicles and clothes belonging to people travelling between sites.

Related measures to control foot and mouth disease include covering disinfectant footbaths between uses so they are not diluted by rain. You should also prevent cattle from coming into contact with animals that cannot develop the disease, but can transmit infected material - for example, dogs, cats, poultry and foxes.

You can limit bovine tuberculosis transmission by deterring badgers from entering properties - for example with yard dogs, water jets or pigs - and ensuring that feed containers are sealed to prevent contamination.

Other control measures include the control of fallen stock - animals that die on your farm because of accident or disease. These control measures are of particular relevance to the control of bovine spongiform encephalopathy. Carcasses are classed as animal by-products and must be disposed of under the rules of the National Fallen Stock Scheme or by an approved private contractor.

See the guide on fallen stock.


Pig biosecurity procedures must be of a high standard to prevent the spread of infectious diseases such as swine influenza. Pig farmers should:

  • prohibit unnecessary visitors to the farm
  • cleanse and disinfect any shared equipment before it enters and after it leaves your premises
  • make sure that personnel in contact with pigs at different premises take standard precautions, such as cleaning and disinfecting boots and clothing
  • prevent people with flu-like symptoms coming into contact with pigs

Download pig biosecurity information from the Defra website (PDF, 895K).

Find out about how to control the spread of swine flu on the Defra website.

Sheep and goats

Sheep and goat biosecurity control follows the general principles of controlling movements of people and livestock, as well as disinfecting vehicles, equipment, clothing and footwear. Diseases of sheep and goats may not always be apparent in the early stages, so stock keepers should regularly monitor their animals for signs of illness.

As with cattle, fallen sheep and goats should be treated as animal by-products and disposed of using standard fallen stock procedures.

Read about disease prevention and control for sheep and goats in the guide on sheep and goat health.


Poultry farmers can increase the biosecurity of flocks through standard control measures, such as washing hands after handling birds and disinfecting boots when travelling between farms.

Poultry-specific measures include:

  • use of disposable protective clothing where practicable
  • providing clean drinking water and food - preferably indoors to prevent contamination by wild animals
  • isolating new birds
  • having a plan for bringing a flock indoors if necessary
  • cleaning and disinfecting housing at the end of each cycle

Commercial poultry farmers should also follow salmonella control principles as part of the National Control Programme (NCP) for the disease. This involves providing Defra with the registration details of your business and the number of birds and flocks you have. You must also comply with sampling procedures such as boot and sock swabs.

Read about biosecurity measures for poultry farmers in the guide on poultry health.


Biosecurity measures specific to deer - whether farmed, park or wild - include health monitoring for notifiable diseases such as:

  • foot and mouth disease
  • bovine tuberculosis
  • bluetongue
  • epizootic haemorrhagic virus disease

It is also important to limit or prevent contact of deer with neighbouring livestock, and to be aware of the health status of any animals bought or sold.

Read about deer health and disease prevention in the guide on deer health, welfare and movement.

Disinfectant procedures for animal diseases

Disinfection is one of the main biosecurity measures to control the spread of animal diseases. Equipment, vehicles, protective clothing and footwear must all be cleaned and disinfected before and after contact with farm animals. Disinfectants can also be used as biosecurity barriers for vehicles and people at farm entrances.

Before disinfecting structures such as sheds, you should clean them with detergents to remove organic matter and oily films.

Disinfectants should be applied under low pressure, for example from a backpack sprayer.

Download information about pig cleaning and disinfection from the British Pig Executive website (PDF, 362K).

Download guidance on cleaning stores, sheds and silos from the Health & Safety Executive (HSE) website (PDF, 75K).

List of approved disinfectants

The AHVLA maintains a list of approved disinfectants for use in farming. The information provided includes supplier addresses and statutory dilution rates for use during control orders for:

  • foot and mouth disease
  • swine vesicular disease
  • poultry diseases, including avian influenza
  • tuberculosis
  • other diseases

Find a list of approved disinfectants on the Defra website.

Disinfecting livestock vehicles

There are special procedures which apply when disinfecting vehicles used to transport farm animals. For example, you must:

  • clean and disinfect vehicles as soon as possible after use involving animals
  • clean wheel arches and mud flaps

Drivers of empty, dirty vehicles leaving markets or slaughterhouses must complete a form to declare where their vehicles will be taken for cleaning.

Find out about cleaning and disinfection of livestock vehicles on the Defra website.

Disinfectants and worker safety

You must ensure that farm workers use disinfectants safely, according to the agricultural Control of Substances Hazardous to Health regulations.

As well as exposure to disinfectants, these cover hazards from cleaning - for example dust from animals - diseases such as leptospirosis, and cleaning in confined spaces.

Read about safety procedures for agricultural employees working with hazardous substances on the HSE website.

Find out how to use pesticides safely on the HSE website.

Exotic disease control contingency plans

Exotic diseases are those not normally found in the UK, such as avian influenza and zoonoses. By contrast, endemic diseases - such as tuberculosis in cattle - are always present. Both types are notifiable to the AHVLA.

Defra has prepared a framework contingency plan to control exotic animal diseases with significant health or economic impact, for example:

  • foot and mouth disease
  • avian influenza
  • Newcastle disease
  • classical swine fever

The government’s contingency plan includes:

  • an alert system for signs of notifiable diseases
  • a notification map of disease outbreaks
  • strategic, tactical and operational procedures
  • a National Disease Control Centre coordinating role

If you notice signs of any notifiable disease in your livestock, you must report them immediately to your local AHVLA office.

Avian notifiable measures

Poultry farmers should be alert for signs of notifiable avian diseases such as avian influenza (bird flu) and Newcastle disease, and should report signs immediately to their vet and local AHVLA office.

For contact details of your local AHVLA office use the postcode search tool on the Defra website.

If avian influenza is subsequently confirmed on the premises, Defra will order measures such as:

  • destruction of birds and eggs on commercial premises
  • disinfection of buildings
  • establishment of a protection zone (three kilometres) and surveillance zone (ten kilometres) from the outbreak point

Download avian influenza control measures information from the Defra website (PDF, 573K).

Importing birds from abroad

Imports of live poultry and hatching eggs are controlled by the AHVLA through the Trade Control and Expert System (TRACES), which issues animal health certificates and related documentation. All such imports must be accompanied by an animal health certificate.

Birds imported from approved third countries outside the EU must be quarantined for 30 days in an approved centre.

The Imports of Products, Animals, Food and Feed System (IPAFFS) will replace TRACES from 1 January 2021.

Read more about quarantine procedures for captive birds imported into the UK.

Poultry Health Scheme

UK poultry producers must be members of the Poultry Health Scheme for at least six weeks before they can export more than 20 birds or hatching eggs to EU countries.

Read about the poultry health scheme in the guide on poultry health.

Control of fresh meat during an animal disease outbreak

Fresh meat products are subject to special control measures during outbreaks of animal diseases, under the Products of Animal Origin (Disease Control) (England) Regulations 2008.

The regulations cover the following diseases:

  • African swine fever
  • classical swine fever
  • Newcastle disease
  • peste des petits ruminants (sheep and goat plague)
  • rinderpest
  • swine vesicular disease

Separate regulations apply to cases of foot and mouth disease and avian influenza.

The AHVLA officers can designate premises as affected by disease. Alternatively, the food business operator - the person responsible for compliance with the requirements of food laws - can apply for a designation.

Meat from establishments where a disease outbreak is suspected or confirmed may not enter the human food chain. Instead, it must be disposed of by slaughterhouses as a Category 2 animal by-product, ie high-risk material containing potential contamination.

See the guide on dealing with animal by-products.

Meat from protection and surveillance zones

Meat from animals in protection or surveillance zones is classed as ‘restricted meat’. It must be kept separate from other meat products, and is subject to special hygiene and labelling regulations.

Find out about treatment and movement of restricted meat on the Defra website.

See the guide on disease notification and restrictions.

Meat and milk hygiene measures during outbreaks

Special hygiene measures apply to meat and milk food products during outbreaks of animal diseases.

Meat hygiene measures

‘Restricted meat’ is meat from animals within the designated protection or surveillance zones. Such meat must:

  • be marked as ‘restricted meat’
  • be kept separately from other meat at all times
  • be transported separately and only to designated premises
  • not be traded or sold in the UK
  • not be traded with other EU states
  • not be exported from the EU

Find out about regulations governing the treatment and movement of restricted meat on the Defra website.

Restricted meat can be transported to a designated treatment centre for an approved treatment to make it safe. After treatment, the meat is considered normal and the restricted markings can be removed.

Milk hygiene measures

During disease outbreaks, milk and milk products from affected areas cannot be sold for human consumption or exported.

If cattle show signs of disease, their milk and milk products must be treated and disposed of as Category 2 animal by-products (ABPs). The products must be collected and transported in leak-proof covered vehicles and kept separately from other ABPs.

Download Defra’s guidance on the collection and disposal of milk and milk products not intended for human consumption from the Agricultural Document Library (ADLib) website (PDF, 47K).

See the guide on dealing with animal by-products.

Restocking cattle herds and sheep flocks

Restocking herds after an outbreak of disease requires careful planning, assessment of health records and compliance with livestock movement regulations. This helps reduce the possibility of a recurrence of the disease.

Restocking cattle herds

If you are buying or selling a cattle herd, you should:

  • develop a herd health plan with a vet
  • assess (if buying) or provide (if selling) written evidence of outbreaks among the herd
  • check the herd’s tuberculosis testing records
  • establish that importers have complied with the relevant regulations

Download Defra’s guidance on restocking cattle herds from the ADLib website (PDF, 63K).

Restocking sheep flocks

If you are selling a sheep flock or buying a replacement one, you should:

  • comply with livestock movement regulations
  • develop a flock health plan with your vet
  • provide (if selling) or assess (if buying) written evidence of any diseases within the flock
  • consider the possibility of scrapie, with reference to the National Scrapie Plan
  • comply with all import regulations

Download Defra’s guidance on restocking sheep flocks from the ADLib website (PDF, 32K).

Protecting employees from infection at work

Farming and food processing businesses should take steps to protect their employees from zoonoses - diseases transmissible from animals to humans. There are about 40 potential zoonoses in the UK. Most are mild and tend to clear up naturally. However, some can cause serious health problems and are notifiable, which means you must report them to your local AHVLA office.

For contact details of your local AHVLA Office use the postcode search tool on the AHVLA website.

Notifiable zoonoses include:

  • anthrax
  • avian influenza
  • bovine spongiform encephalopathy
  • brucellosis
  • equine viral encephalomyelitis
  • glanders and farcy
  • rabies
  • rift valley fever
  • tuberculosis
  • West Nile virus

Non-notifiable zoonoses include:

  • coxiella - causing Q fever
  • chlamydia - causing pscittacosis/ovine chlamydiosis
  • toxoplasma - causing toxoplasmosis
  • orf - skin disease of sheep
  • ringworm

Preventative health measures on farms include hand-washing facilities - these are especially important for visitors and open farms.

Download information about preventing ill health at open farms from the HSE website (PDF, 83K).

Protection from bovine tuberculosis

There are three main ways by which bovine tuberculosis (TB) can be transmitted to humans:

  • drinking raw milk from cows with ‘disseminated TB’ - cows with TB that has spread outside the lungs or which have TB lesions on udders
  • close proximity to animals with TB lesions in the lungs or infected cattle carcasses
  • infection through cuts or abrasions in the skin

Find out how the risk of bovine TB transmission to humans can be reduced on the Health Protection Agency website.

You can also take steps to protect stored feed from being contaminated by badgers that are infected with TB.

Organisations that can help

You can get further information and advice on controlling disease in farmed animals from the following organisations.

The AHVLA is an executive agency of Defra. It is responsible for ensuring farmed animals in England and Wales are healthy, free of disease and properly cared for.

Find out about the AHVLA on the Defra website.

The HSE is a government agency responsible for preventing death, injury and sickness to those at work or affected by work-related activities.

Find out about the role of the HSE in the agricultural sector on the HSE website.

The Food Standards Agency helps farmers and producers ensure the safety of products entering the human food chain.

Find out how farmers and growers can maintain the safety of food products on the Food Standards Agency website.

Defra helps the farming industry to operate as efficiently as possible. Defra administers European support policies that provide around £3 billion to UK agriculture. Defra oversees a number of agencies that work with farmers, supervise imports and exports of crops, and implement pest and disease controls. You can call the Defra Helpline on Telephone 08459 33 55 77.

In England, the Farm Advisory System advises farmers about cross compliance. For further information, call the Cross Compliance Helpline on Telephone 0845 345 1302.

Alternatively, find information on cross compliance requirements on the Cross Compliance website.

The National Farmers Union (NFU) represents the farmers and growers of England and Wales. It aims to promote successful and socially responsible agriculture and horticulture, while ensuring the long-term viability of rural communities.

You can phone NFU Callfirst Helpline on Telephone 0870 845 8458, or find out about the NFU’s work on the NFU website.

Further information

NFU Callfirst Helpline

0870 845 8458

AHVLA Information Line

0844 884 4600

Defra Helpline

08459 33 55 77

Biosecurity and good hygiene guidance on the Defra website

Contingency plans for controlling farmed animal diseases on the Defra website

Pesticides safety guidance on the HSE website

Approved disinfectants information on the Defra website

Livestock vehicle cleansing and disinfection information on the Defra website

Download cleaning stores, sheds and silos guidance from the HSE website (PDF, 75K)

Download Defra’s framework response plan for exotic diseases from the Agricultural Document Library website (PDF, 1.30MB)

Exotic disease control contingency plan

Avian influenza information

Avian quarantine information on the Defra website

Animal health certificate applications using TRACES guidance on the Defra website

Restricted meat treatment and movement regulations guidance on the Defra website

Hygiene regulations for livestock being presented for slaughter on the Food Standards Agency website

Download Defra’s milk and milk products collection and disposal guidance from the ADLib website (PDF, 47K)

Download Defra’s restocking cattle herds guidance from the ADLib website (PDF, 63K)

Download Defra’s restocking sheep flocks guidance from the ADLib website (PDF, 32K)

Infection at work prevention advice on the HSE website

Download guidance on common zoonoses and how to protect employees and visitors from the HSE website (PDF, 84K)

Zoonoses prevention advice on the Defra website

Published 18 September 2012