The overall success of the programme of iodine prophylaxis in many parts of the world is to be commended and the highly laudable efforts of responsible governments and non-governmental organizations should be encouraged and supported. Although the long-term effects of iodine deficiency are gradually being eliminated, large scale and often unsupervised salt iodination has produced undesirable effects which need to be highlighted in order to minimize damage to public health. We discuss the effects of iodine in the initiation and propagation of thyroid autoimmunity and highlight epidemiological, laboratory and clinical data that provide clues to the influence of iodine on thyroid autoimmunity.