INTRODUCTION. Functional somatic symptoms are commonly encountered among paediatric patients. Even so, little is known about the current treatment practice. We aimed to explore the current organisation of clinical care for children and adolescents with functional somatic symptoms in a hospital setting. METHODS. A de novo questionnaire with 60 items about practice patterns for children and adolescents with functional somatic symptoms was developed, tested and distributed to all Danish paediatric departments. RESULTS. All 19 paediatric departments in Denmark participated. Two departments had no available treatment programme, whereas the remaining 17 departments offered a treatment programme. Overall, substantial variation was reported in the number of patients in treatment, the composition of multidisciplinary teams and in the tasks and training of these teams. A future increase in paediatric patients with functional somatic symptoms was expected by 95% of the departments. Still, 59% reported a reduction in resources allocated to this group over the past five years. Two thirds of the departments expressed a need for clinical guidelines. CONCLUSIONS. Substantial variation was observed in the healthcare services offered to paediatric patients with functional somatic symptoms referred to the Danish hospital setting. Clinicians called for guidelines, which, in the light of the decreasing resources allocated and the increasing patient numbers, may help ensure a systematic approach and better quality of care for this patient group.