It has been suggested that feeding practices in infancy may affect the development of various autoimmune diseases later in life. Since thyroid alterations are among the most frequently encountered autoimmune conditions in children, we studied whether breast and soy-containing formula feedings in early life were associated with the subsequent development of autoimmune thyroid disease. A detailed history of feeding practices was obtained in 59 children with autoimmune thyroid disease, their 76 healthy siblings, and 54 healthy nonrelated control children. There was no difference in the frequency and duration of breast feeding in early life among the three groups of children. However, the frequency of feedings with soy-based milk formulas in early life was significantly higher in children with autoimmune thyroid disease (prevalence 31%) as compared with their siblings (prevalence 12%; chi 2 = 7.22 with continuity factor; p less than 0.01), and healthy nonrelated control children (prevalence 13%, chi 2 = 5.03 with continuity factor; p less than 0.02). Therefore, this retrospective analysis documents the association of soy formula feedings in infancy and autoimmune thyroid disease.