Enuresis and encopresis can be stressful for children and parents. We investigated the comorbid psychiatric disorders and the emotional and behavioral symptoms associated with elimination disorders. A total of 97 children and adolescents (aged 4–17 years) with an elimination disorder participated in this study. The elimination disorder group consisted of three subgroups: 50 subjects with enuresis nocturna, 26 with encopresis, and 21 subjects with enuresis+encopresis. The control group with no elimination disorder comprised 50 healthy subjects. All children were interviewed by a child and adolescent psychiatrist. Comorbid psychiatric disorders were assessed using the Schedule for Affective Disorders and Schizophrenia for School-Age Children-Present and Lifetime version (K-SADS-PL). Parents completed the Strengths and Difficulties Questionnaire. The most common diagnosis was attention-deficit/hyperactivity disorder, followed by oppositional defiant disorder. The highest rate of psychiatric comorbidity was observed in the enuresis+encopresis subgroup, followed by the enuresis nocturna and encopresis subgroups. All the subgroups had higher total difficulties scores than the control group. Screening for psychiatric disorders should be performed for all children with incontinence.