Background: Congenital disorders of glycosylation (CDG) form a group of inherited metabolic diseases. Although the clinical presentation shows extreme variability, the nervous system is frequently affected. Several parents of our patients diagnosed with CDG reported behavioral problems, including mood swings, depressive behavior, and anxiety. This raised the question whether patients with CDG have an increased risk for socio-emotional problems. Methods: We evaluated 18 children with confirmed CDG. The Child Behavior Checklist (CBCL) was used to screen for socio-emotional problems. To determine the disease progression and severity in CDG, the Nijmegen Paediatric CDG Rating Scale (NPCRS) was used. Results were compared to “norm scores” and to children with mitochondrial disorders and children with other chronic metabolic disorders with multisystem involvement. Results: Results showed a high prevalence of socio-emotional problems in children with CDG. Mean total scores, scores on withdrawn/depressed behavior, social problems, and somatic complaints were significantly increased. More than two thirds of our CDG patients have abnormal scores on CBCL. The mean score on social problems was significantly higher compared to our two control groups of patients with other chronic metabolic disorders. Conclusions: Patients with CDG have an increased risk of developing socio-emotional problems. A standard screening for psychological problems is recommended for the early detection of psychological problems in CDG patients.