The aim was to study whether cow-milk-free diet during the last trimester of pregnancy influences the development of diabetes-related autoantibodies in nondiabetic children. We also examined the effect of later introduction of cow milk proteins and gluten. Blood samples were taken from 205 children at 6 weeks, 6 months, 18 months, and 5 years, whose mothers had been randomized to either a cow-milk-free diet or not during the last trimester of pregnancy. During the first 3 months of life, cow milk proteins were not fed to the children. Autoantibodies against GAD.(65) (GADA), tyrosine phosphatase (IA-2A), and insulin (IAA) were determined by a radioligand-binding assay. We found specific autoantibodies, although in low concentrations below the traditional cutoff for positivity in the children. The diet of the mother during pregnancy had no influence on development of autoantibodies, nor did duration of breast-feeding or time for introduction of gluten. Cow milk introduction between 3 and 6 months caused a transient increase in GADA at 6 months of age (p < 0.05). Children who developed atopic disease had significantly lower IA-2A at 6 months (p < 0.001).