Aim: Study of the prevalence of autoimmune (AI) disorders among children at diagnosis of coeliac disease (CD) and after gluten free diet (GFD). Methods: We enrolled 236 children (152 F, 84 M; mean age 66 ± 48 months) with CD diagnosed by serological markers and typical hystological lesions. 149 (96 F, 53 M; mean age 61 ± 44 months) were followed for a mean time of 43 ± 30 months (range 12-118). All were in complete remission on a GFD. 220 age-matched children who underwent gastroscopy for dyspepsia or abdominal pain served as controls. All had normal intestinal histology and no serological markers of CD. All patients and controls were tested for the presence of organ and non-organ specific autoantibodies (Abs) and were investigated for the presence of AI diseases. Statistical analysis was performed by Chi-square test. A p value <0.05 was considered to be significant. Results: Of the 236 children, 54 (22.9%, 41 F, 13 M) had clinical or latent (i.e., only serological) AI disorders at CD diagnosis vs 1.4% of controls (p < 0.0001). 24 (10.2%) had clinical AI diseases: 10 had type 1 diabetes mellitus (T1DM), 6 Hashimoto's thyroiditis (HT), 2 HT+T1DM, 2 juvenile chronic arthritis, 2 alopecia, 1 vitiligo, 1 AI thrombocytopenia, while 30 (12.7%) had Abs without clinical manifestations: 12 had antinuclear Abs (ANA), 10 thyroid Abs, 4 parietal cell Abs (PCA), 2 PCA+ANA, 1 PCA+ islet cell Abs (ICA), 1 ICA+ANA. Among the 149 children followed, 37 (24.8%) had AI disorders at diagnosis of CD. 16 patients (10.7%) had clinical AI diseases, while 19 (12.7%) had latent AI disorders. At the end of the follow-up, 48 (32.2%) had clinical or latent AI disorders (p = 0.2): 14 (9.4%) had clinical (p = 0.8) and 34 (22.8%) had latent autoimmunity (p = 0.07). Summary: The prevalence of AI disorders is significantly increased among children at diagnosis of CD. Over a period of GFD, clinical AI diseases did not increase, while latent autoimmunity showed a trend to increase. Conclusion: The prevalence of AI disorders is much higher in children at diagnosis of CD. GFD seems to hold back the development of new clinical AI diseases despite an increase in serological autoimmunity.