Somatoform disorders (SD), commencing during adolescence, represent a major problem in health care systems. While literature underlines the high presence of mental health problems among children and adolescents afflicted by somatic symptoms in the general population, limited evidence is available on the prevalence of comorbid somatic symptoms in child and adolescent psychiatric populations. We assessed the prevalence of somatic symptoms, depression, and anxiety by validated questionnaires in an inpatient cohort. We further screened for the presence of SD. Out of 434 inpatients aged 11–17 years, 371 were included and a total of n = 288 (77.6%) children and adolescents participated in the study. A total of 93.8% of the inpatients reported somatic symptoms within the past six months and still almost half (45.7%) of the sample reported at least one somatic symptom within the last seven days prior to inquiry. Relating to the past six months, 59.5% were positively screened for SD, and 44.6% reported symptoms eligible for positive screening within the past seven days prior to the survey. Somatoform symptomatology was highly associated with anxiety and depression scores, but functional decline was amenable to the number of somatic symptoms only. We provide evidence that somatic symptoms are frequent in children and adolescents being treated in child and adolescent psychiatry and are relevant to everyday functioning. Screening for somatic symptoms should be introduced in the routine diagnostic procedures for early detection of SD in the commencing stages.