The aim of this study was to evaluate the prevalence of thyroid autoantibodies and clinical significance of thyroid autoimmunity in children with the diagnosis of diabetes mellitus type 1. The study group comprised 222 children all with newly diagnosed diabetes mellitus type 1 (122 boys) with a mean age 9.92 ± 4.5 years, who were admitted to a regional diabetes division in 2000–2004. Assessment of ATA and ATG were performed and two emerging groups—ATA/ATG (+) and ATA/ATG (−) were compared, including anthropometric data, HbA_1C, plasma lipids, TSH, fT4. Positive antibodies titre was found in 27 (12.16%) of the children. Apart from older age in the antibody positive group (11.67 vs. 9.67 years, p < 0.05), there were no significant differences among these groups regarding other clinical and laboratory characteristics. Concluding, the presence of thyroid autoantibodies in 12.16% of subjects with newly diagnosed diabetes confirms the necessity of screening of all children, especially adolescents from the time of diagnosis of diabetes mellitus type 1 onwards. No association between existence of autoantibodies and the clinical status of a child at the presentation of diabetes was demonstrated by this study.