Background The need for screening for autoimmune thyroid disease in children who have HLA-conferred susceptibility to type 1 diabetes (T1D), but have not yet been diagnosed with T1D, has not been thoroughly studied. The aim of this study was to describe the prevalence of positive thyroid peroxidase antibodies and its effect on thyroid function in children with genetic susceptibility to T1D as well as to describe the association between thyroid autoimmunity and HLA-DQ genotypes. Methods Cross-sectional study in 223 children (112 boys) aged 7.4-10.5 years with HLA-conferred susceptibility to T1D. TPOAb were measured in all children; thyroglobulin antibodies (TGAb) and thyroid function in TPOAb positive subjects. Results Girls had a significantly higher median TPOAb concentration than boys (12 vs 11 kU/L; p=0.001). Positive TPOAb occurred in 13.9% and positive TGAb in 4% of subjects. Only two children had mild changes in thyroid function. There was no association between HLA risk groups and the prevalence of TPOAb. Conclusions TPOAb are common in children with HLA-conferred susceptibility to T1D, yet are weakly associated with thyroid function, suggesting limited value of thyroid screening in this cohort.