The primary cause of encopresis is unclear. A variety of explanations have been proposed—psychological, anatomical, physiological and dietary—but the most likely explanation is that the causes of encopresis are multifaceted. Most children with encopresis do not have a physical abnormality that interferes with their ability to gain bowel control. Some children may intentionally withhold for psychological reasons; they may fear using the toilet or the withholding may be due to a pattern of oppositional behavior.

In many cases encopresis occurs when there is a stressful family situation, such as divorce, birth of a sibling or a transition such as starting school. When a child actually smears feces, there is a strong indication that there may be a problem in family relationships. The child who is reluctant to openly express anger may express it by soiling. Soiling may occur in a child who has had a traumatic or frightening experience, such as sexual or physical molestation. When behavior problems occur they are usually due to the social consequences of soiling.

The physiological basis of encopresis is chronic or intermittent retention of feces, resulting in distension of the rectum and colon leading to a lack of sensitivity for the defecation reflex. The stools become large and hard, and attempted passage may result in pain and avoidance of the toilet, which make the situation worse. Rectal impaction may result, and the watery contents of the higher colon are passed around the retained stool, resulting in involuntary soiling.

Other physiological factors that may contribute to constipation include dehydration due to febrile illness, hypothyroidism, or a medication side effect. Overflow incontinence resulting from constipation can be caused by faulty nutrition, structural disease of the anus, rectum and colon, or endocrine or neurological disorders.