Although a few children experience encopresis because of malformations of the lower bowel and anus or irritable bowel disease, most have no physical problems to explain this disorder. Constipation is present in about 80% of children who experience involuntary encopresis. As feces moves through the large intestine, water is removed. The longer the feces stays in the large intestine, the more water is removed, and the harder the feces becomes. The result can be hard or painful bowel movements. In response, children may start to hold back when they feel the urge to eliminate in order to avoid pain. This starts a cycle of constipation that results in retentive encopresis.

Once elimination is avoided, the bowel becomes full of hard feces. This stretches the large intestine. Eventually the intestine becomes so stretched that liquid feces backed up behind the blockage is able to leak around the hard feces. Children with this type of encopresis do not feel the urge to have a bowel movement and are often surprised when their pants are stained with foul smelling liquid feces. This leakage of feces is called overflow incontinence. Parents sometimes mistake this soiling for diarrhea, because the feces expelled is liquid. Every so often, children with involuntary encopresis may pass large stools, sometimes with volumes big enough to clog the toilet, but the relief this brings is temporary.

Although about 95% of encopresis is involuntary, some children intentionally withhold bowel movements. The American Psychiatric Association (APA) recognizes voluntary encopresis without constipation as a psychological disorder. This disorder is said to occur when a child who has control over his bowel movements chooses to have them in an inappropriate place. The feces is a normal consistency, not hard. Sometimes it is smeared in an obvious place, but it may also be hidden from adults.

Voluntary encopresis may result from a power struggle between caregivers and the child during toilet training, or the child may have developed an unusual fear of the toilet. It is also associated with oppositional defiant disorder (ODD), conduct disorder, sexual abuse, and high levels of psychological stress. For example, children who were separated from their parents during World War II were reported to have a high rate of encopresis. However, parents and caregivers should be aware that very few children soil intentionally and most do not have a behavioral or psychological problem and should not be punished for their soiling accidents.