The origins of autoimmunity are still elusive despite significant advances in immunology. There is cumulative evidence that, beyond simple genetics, the maternal environment plays a critical role in the development of common autoimmune disorders, such as multiple sclerosis or diabetes. In recent years, the trafficking of maternal cells to the offspring has been clearly demonstrated. This microchimerism represents the very first immunological event in fetal life. The number of persisting maternal cells has been associated with several autoimmune disorders such as systemic sclerosis, juvenile dermatomyositis and diabetes. The precise role of the maternal cells in these disorders remains unclear. Based on recent experimental work in an animal model of juvenile diabetes, we will discuss the possibility of maternal cells modifying the response of the developing fetal immunity towards self.