Coeliac disease is a chronic immune-mediated systemic inflammatory disease triggered by gluten ingestion in genetically predisposed individuals. Clinical picture ranges from gastrointestinal to extraintestinal manifestations. Genetic predisposition is related to the presence of HLA-DQ2 and DQ8 heterodimers, also connected to a higher risk of the occurrence in other autoimmune conditions, most commonly diabetes type 1 (DM1). The aim of this study was to investigate clinical, biochemical and immunogenetical characteristics of patients with coeliac disease diagnosed at the Department of Paediatrics at University Hospital Centre Zagreb. The data collected retrospectively from medical records from 2008 to 2018 included age at the time of diagnosis, clinical presentation, results of antibody testing, small bowel biopsy and HLA typing. A total of 55 patients were enrolled, 29 females and 26 males (1.12:1), mean age 11.7 ± 4.62 years. The classical form of coeliac disease (diarrhoea, abdominal distension, failure to thrive) was found in 22 out of 55 patients (mean age of diagnosis 3.41 years). In 18 patients with atypical presentation mean age at the time of diagnosis was 9.31 years. The asymptomatic disease was found in 15 patients, mostly with newly diagnosed diabetes type I. Out of 39 patients who underwent HLA typing, 36 patients were positive for either single or double dose of DQ2.5 or DQ8 HD. Patients at very high risk according to HLA typing were mainly asymptomatic, 8 out of 17 were patients with DM1. There were two patients with autoimmune thyroiditis, one at very high risk and one at high risk. Clinical presentation according to age was similar to the general population of patients with coeliac disease, most common symptoms in the youngest age group being typical gastrointestinal. Considering HLA-DQ heterodimer frequency, our patients have a similar distribution to other European and non-European patients with coeliac disease. However, since many patients with a very high risk of developing coeliac disease according to HLA typing were patients with DM1, we would like to emphasize the importance of screening for coeliac disease in this group of patients.