This study was undertaken to gain insight in the clinical spectrum of paediatric coeliac disease (CD) in a Dutch teaching hospital. We retrospectively compared the frequency of CD in children with a wide spectrum of complaints with and without CD antibodies in serum and were interested if certain complaints are more pathognomonic for CD. Furthermore, we expected that over a period of 10-year incidence rates of CD would have increased and shifted towards an atypical presentation with more non-gastrointestinal symptoms with increasing age. A retrospective, single-centre, case-control study was performed. All patients who presented at the Department of Paediatrics, Tergooi Hospital, with symptoms suspected for CD were eligible for inclusion during the study period from 1 January 2007 till 31 December 2016. Children were diagnosed with CD according to the 2005 and 2012 ESPGHAN guideline between 2007 and 2016, respectively. Demographic data, presenting symptoms, prevalence of associated conditions and serology results were examined. A total of 105 new cases of paediatric CD were observed, with an average of 10 new cases each year. The calculated incidence was 21.09 (CI 17.49–25.22)/100,000 under 18 years of age. About 40% were infants and toddlers, predominantly presenting with gastrointestinal symptoms. Primary and high school children had more display of atypical symptoms (p = 0.001, p = 0.017) and nongastrointestinal symptoms (p = 0.009, p = 0.009) than infants and toddlers. In 8.6% of the CD patients, mostly primary school aged female patients, the serology was repeated at least once in time to become positive. The median time for serology to become positive was 609 days (range 140–1054). Conclusion: As it is well known, our study supports the increasing notion of a shift in the clinical spectrum of presenting symptoms in paediatric CD towards an atypical presentation, with more non-gastrointestinal symptoms and a diagnosis at a later age in a Dutch population, whereas the number of new cases did not increase over the years.