The immune system is a complex group of cells, tissues and organs that recognize and attack foreign substances, pathogenic organisms and cancer cells. It also responds to injury by producing inflammation. The immune system has peripheral components that include skin-associated lymphoid tissues (SALT) and mucosa-associated lymphoid tissues (MALT), located where pathogens and other harmful substances gain access to the body. Phototherapy, delivered at appropriate treatment parameters, exerts direct actions on the cellular elements of the peripheral part of the immune system since it is readily accessible to photons. The more deeply located components of the immune system, such as the spleen, thymus, bone marrow and many of the lymph nodes, respond to phototherapy indirectly via changes elicited in the peripheral components. All the components of the immune system are linked by lymphatic vessels and blood vessels, many of the capillaries of which are located in the sub-epithelial connective tissues of the skin and mucous membranes. The location of these capillaries, particularly those in the skin and oral mucosa, provides photons with ready access to the cells and molecules in transit through them. These cells and molecules, some modified by exposure to the photons, then travel to deeper components of the immune system and can affect their activity. In addition to having direct effects on the peripherally located cells of the immune system, photons can thus also produce indirect effects on immune cells that are too deeply located for the photons to affect them directly. For example, cytokines released from peripheral immune cells in response to the direct action of photons can be transported to and affect immune cells that have not been exposed to photons. Examples of investigations into the direct and indirect effects of phototherapy on the components of the immune system are cited below. The immune cells communicate by the exchange of chemical messengers termed cytokines, some of which act as switches that can turn certain cell types on or off while others attract immune cells to areas of infection. Phototherapy can affect the synthesis and release of cytokines. The importance of treatment parameters and the metabolic status of the target cells in determining outcome are emphasized. The clinical significance of the effects of phototherapy on the immune system is considered and future research proposed.