Although laser irradiation is becoming common practice in medicine, there is not always a clear understanding of the possible side-effects. The present report is a light and electron microscopic study of the effects of fixed low intensity doses of soft HeNe laser on the thyroid of Wistar rats. The immediate effects are mild multifocal degenerative changes; these lesions recover in less than 3 months. Long-term lesions are identified only by electron microscopy; they consist of an increased number of peroxisomes and free or intramitochondrial crystalline structures. We discuss the laser's hypothetical functions.