Coeliac disease is characterized by a wide array of clinical presentations. The focus of our study was to comprehensively assess the clinical manifestations of coeliac disease in newly diagnosed children in Slovenia. Our objectives include estimating the incidence of the disease in children in 2022. In this prospective study, Slovenian paediatric gastroenterologists were invited to provide patient data using medical records of children under 19 diagnosed with coeliac disease from March 2021 to October 2023. Patient data were collected through a dedicated web-based form adapted from the CD SKILLS project, including data on clinical manifestations and laboratory results. Furthermore, the study included an estimation of the incidence of coeliac disease in children and adolescents in Slovenia in 2022. Analysis involved data from 160 children and adolescents (median age: 8 years; 61.9% female). Overall, 16.9% were asymptomatic at diagnosis and 29.4% belonged to a high-risk group for coeliac disease. Among symptomatic cases ( N = 133), abdominal pain was the leading symptom (44.4%), followed by anaemia (12.0%) and diarrhoea (10.5%). Malabsorption symptoms were more prevalent in very young children. Anaemia was found in 22.8 and 10.7% had abnormal alanine aminotransferase levels. The estimated incidence of coeliac disease in Slovene children in 2022 was 17.5/100 000. Abdominal pain emerged as the primary symptom of coeliac disease in children and adolescents, except in very young children where malabsorption symptoms were predominant. Our observation of a lower prevalence of abnormal liver function tests suggests subclinical coeliac disease may be less common in children. Moreover, the calculated coeliac disease incidence in Slovenia aligns with existing data.