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Abstract Background This naturalistic study assesses the effectiveness of inpatient multidisciplinary treatment of children and adolescents with somatic symptom disorders (SSD) and investigates the role of pain coping strategies and psychiatric comorbidity (anxiety, depression). Methods Sixty children and adolescents (mean age 14.4 years) with SSD who underwent inpatient multidisciplinary treatment were assessed regarding their school attendance, levels of discomfort, coping strategies and psychiatric comorbidity (depression, anxiety) at pretreatment, discharge and 6 months following treatment. Results At discharge, the children and adolescents reported improvements in their level of discomfort, psychiatric comorbidities (anxiety, depression) and pain coping strategies, with medium to large effect sizes. Six months following treatment, the improvements remained stable, including significantly higher school attendance rates (d = 1.6; p < 0.01). Improvement in pain coping was associated with increased school attendance. Conclusion Inpatient multidisciplinary treatment is effective in reducing levels of discomfort, psychiatric comorbidity (anxiety, depression), and school absence and in improving coping strategies.