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Rarely, encopresis is caused by an anatomic abnormality or disease that the child is born with. In the vast majority of cases, encopresis develops as a result of chronic (long-standing) constipation.

Many people think of constipation as not passing a bowel movement every day. However constipation implies not only infrequent bowel movements, but also having difficulty in passing bowel movements and/or experiencing pain with the passage of stools. In most cases of childhood constipation, the constipation develops after the child experiences pain when passing stools.

• Each person has his or her own schedule for bowel movements, and many healthy people do not have a bowel movement every day.
• A constipated child might have a bowel movement every third day or less often.
• Most importantly, a constipated child tends to pass large and hard stools and experience pain while doing so.

In most children with encopresis, the problem begins with the passage of large stools and/or having pain while passing stools. This often happens long before the encopresis starts, and the child may not remember this when asked.

• Over time, the child becomes reluctant to pass stools and "withholds it" to avoid the pain.
• This "witholding" of stool becomes a habit that often persists long after the constipation or pain with bowel movements has resolved.

• As the colon stretches more and more, the child loses the natural urge to have a bowel movement.
• Eventually, looser, partly formed stool from higher up in the intestine begins to leak around the large collection of harder, more formed stool at the lower part of the colon (rectum) and then leaks out of the anus (the opening from the rectum to the outside of the body).
• Often in the beginning, only small amounts of stool leak out, producing streaks in the child's underwear. Typically, parents assume the child isn't wiping very well after passing stools, and they don't worry about the smears.
• As time goes on, the child is less and less able to hold the stool in more and more stool leaks, and eventually the child passes entire bowel movements into his or her underwear.
• Often the child is not aware that he or she has passed stools.
• Because the stool is not passing normally through the colon, it often becomes very dark and sticky and may have a very foul smell.

Over time, the child with encopresis may also develop incoordination of the muscles used to pass bowel movements. In many children, the anal sphincter contracts rather than relaxes when they are trying to push the stools out. This disturbed coordination of muscle function called anismus or paradoxical contraction of the pelvic floor during defecation, makes it very difficult for the child to empty his or her colon when they go to the toilet.

• The most common cause of constipation in children is the passage of large, hard, and painful bowel movements. The child "withholds" to avoid pain. Over time, this results in the bowel movements becoming larger and harder, and a vicious circle begins.
• Some experts believe children become constipated when they do not eat enough fiber, but others believe there is no connection between diet and constipation. There is no clear evidence that constipation is caused by too little fiber in the diet.
• Many doctors think that some children become constipated because they do not drink enough water. However, other doctors question whether the amount of water the child drinks has much of an effect on constipation.
• Constipation does seem to run in certain families.
• For many children, no clear cause of the constipation can be identified.

Encopresis is a very frustrating condition for parents. Many parents become angry at the repeated need to bathe the dirty child and to clean or discard soiled underwear. Many parents assume the soiling is the result of the child being lazy or that the child is soiling intentionally to annoy them. In most instances, this is not the case. Children with encopresis are however significantly more likely to suffer from attention deficit hyperactivity disorder (ADHD) than the general population. It is important to remember that in almost all cases, encopresis is involuntary - the child does not soil on purpose.

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