Aims/Hypothesis. To examine the prevalence of subclinical islet autoimmunity in children from two countries with a twofold to threefold difference in incidence of childhood Type I (insulin-dependent) diabetes mellitus.¶Methods. Sera were collected from 2860 English and 3053 Lithuanian non-diabetic schoolchildren according to the same protocol. Occult diabetes was excluded by blood glucose measurement. Antibodies to GAD and the protein tyrosine phosphatase IA-2 were measured with standardised radiobinding assays in a single laboratory. Islet cell antibodies and insulin autoantibodies were additionally measured in all samples with GAD and/or IA-2 antibody levels above the 97.5^th centile of the English schoolchildren.¶Results. Of Lithuanian schoolchildren 2.7 % had GAD antibodies above the 97.5^th centile of the English schoolchildren but only 0.2 % had antibodies to IA-2 above this threshold (p < 0.001). Islet cell and/or insulin autoantibodies above the 97.5^th centile were found in 22 Lithuanian and 16 English schoolchildren and the overall prevalence of two or more antibodies on or above the 97.5^th centile was similar [0.7 % (0.5–1.1) vs 0.6 % (0.4–1.0)] in the two cohorts.¶Conclusion/interpretation. The prevalence of multiple antibody markers was similar in the cohorts from the two populations, despite the two to three-fold difference in incidence of diabetes. The unexpectedly high prevalence of subclinical islet autoimmunity suggests that the incidence of diabetes in Lithuania is likely to increase in the near future. [Diabetologia (2001) 44: 16–21]