The autoimmune thyroid diseases (AITDs) are multifactorial disease which are caused by genetic susceptibility and environmental triggers. Various epidemiological and genetic techniques can be employed to study the genetic contribution to disease development. Most epidemiologic data support an important genetic contribution to the development of AITD. The genetic susceptibility to AITD involves several genes with varying effects. Some AITD susceptibility genes are most likely immune modifying genes which increase the susceptibility to autoimmunity in general (e.g. HLA, CTLA-4) while others may be thyroid-specific (e.g. thyroglobulin). These genes probably act in concert to increase the autoimmune reactions in susceptible individuals and direct them towards the thyroid.