Vaccines are usually designed to prevent diseases commonly caused by microbes, such as bacteria, viruses, and fungi. Specific pieces (antigens) on these organisms stimulate the body's immune mechanisms in two ways: (a) by eliciting the production of antibodies, large protein molecules called globulins that circulate in the body and recognize, bond to foreign substances, and neutralize or help eliminate foreign substances (humoral immune response); and (b) by generating specialized types of immune cells that act to destroy cells infected by the organisms (cellular immune response). The antibodies are produced by B-Cells (B lymphocytes), which mature in the bone marrow, become plasma cells, and migrate to the spleen and lymph nodes. Highly specialized T Cells (T lymphocytes) mature in the thymus, and give rise to helper T cells and cytotoxic or killer T cells. Both responses act in concert to help control, if not completely rid, the body of the specific infection.

The immune response to vaccination consists of two phases: (a) the first contact or exposure (primary response) to a vaccine produces a low level response of relatively short duration, and (b) the second contact (booster) gives rise to a more rapid, higher level and more prolonged response. This latter response reflects the existence of a larger number of memory cells that are primed to recognize and respond more quickly and effectively when the immune system encounters the organism again.

Traditionally, active immunity has been achieved by administering classical vaccines composed of whole killed (inactivated) organisms or live, weakened (attenuated) organisms that have lost their disease-producing properties. Subunits of the organisms such as an outer coat protein or a toxin inactivated by formalin to become a toxoid are also used. Advances in genetic engineering are being used to improve traditional vaccines, create DNA vaccines, and develop more effective ways to deliver vaccines.