The bird has a very adequate defence mechanism against possible threats to its well-being. Although the system is very complex and contains a lot of different mechanisms, it can be divided in a number of main groups, such as:

- Behaviour
- Feathers/Skin
- Mucus membranes
- Local immune system
- Systemic immune system.

The first 3 are the most important. They keep diseases outside. Only when they are not able to prevent the disease from coming in, that the immune system will respond.

The invader will create a local immune response. Killer type cells, present in the invaded tissue, will destroy the enemy by special enzymes or chemical reactions. In this battle these killer cells will die and release certain immune modulators, which will activate the systemic immune system. Also special messenger cells are activated which will transport the invader to the systemic immune system.

The reaction of the systemic system can be based either on production of antibodies (a protein) or more specific killer cells. Both pathways will occupy the invader's surface and inactivate it. Note that, at the moment of hatch, the day old chicken has an incomplete immune system. Only after 7-8 days that all immune cells are on the right spot in the body and sufficiently matured for their function. Maternal antibodies, transferred by the yolk, have a protective function during this period.

Looking at the most used laboratory techniques, we are only able to measure the amount of antibodies produced against a certain disease. So this is the systemic antibody response. In routine technique, checking the quality/amount of protection by cell immunity is not possible yet. Some diseases create a strong antibody reaction such as Gumboro Disease and Newcastle Disease. Others only trigger production of cell protection such as Marek's disease. Most diseases will stimulate both systems.

Therefore, all these antibody tests for sure can tell us something about a contact with an invader or vaccine but do not fully account for the protection status.

Once the pathogen is destroyed, the immune response has to stop. This process is not fully understood yet but there are quite some diseases (certain types of human rheumatism and in poultry amyloidosis) where this reaction does not stop and the animal keeps on producing antibodies which will pile up in joints and liver and eventually kill the animal itself.

Vaccines are nothing more than weakened invaders for the immune system. The type of vaccine and especially the vaccine carrier/solution in case of injections can influence the type of reaction mechanisms. Good oil-emulsions will stimulate the production of antibodies.

The immune system is quite costly in terms of energy. This is easily noted in SPF and FAPP housing systems. Feed savings of adult broiler breeders (3-4 kg weight) in these types of housing can be up to 25 grams feed per day.

As both the introduction and presence of a disease (even in a weakened form), as well as the bird's immune response to it will cost performance and energy, vaccination must be limited to the necessary and intended protection. Vaccination against diseases that are actually not a threat is very costly, both for the cost of the vaccination itself as well as for the cost of the bird's reaction.