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Congenital and Inherited Disorders of the Digestive System in Horses

By Peter D. Constable, BVSc (Hons), MS, PhD, DACVIM, Dean, College of Veterinary Medicine, University of Illinois
Gordon J. Baker, BVSc, PhD, MRCVS, DACVS, Professor, Equine Medicine and Surgery, College of Veterinary Medicine, University of Illinois
Joseph A. DiPietro, DVM, MS, Vice President for Agriculture, Institute of Agriculture, University of Tennessee
Walter Ingwersen, DVM, DVSc, DACVIM, Specialist, Companion Animals, Boehringer Ingelheim (Canada) Ltd, Vetmedica
John E. Madigan, DVM, MS, Distinguished Professor, Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis
James N. Moore, DVM, PhD, Distinguished Research Professor, Department of Large Animal Medicine, College of Veterinary Medicine, University of Georgia
Michael J. Murray, DVM, MS, Technical Marketing Director, Merial Limited
Sofie Muylle, DVM, PhD, Faculty of Veterinary Medicine, Department of Morphology, Ghent University
Stanley I. Rubin, DVM, MS, DACVIM, Clinical Professor, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign
Susan D. Semrad, VMD, PhD, DACVIM, Associate Professor, Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin
Josie L. Traub-Dargatz, DVM, MS, DACVIM, Professor of Equine Medicine, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University

Congenital abnormalities are conditions that an animal is born with; they are often called birth defects. Some of these conditions are inherited and tend to occur within particular families or breeds, while others are caused by chemicals or injury during pregnancy. For still others, the cause is unknown. The most common congenital abnormalities of the digestive tract in horses are described below.


A cleft palate or cleft lip (harelip) is caused by a defect in the formation of the jaw and face during embryonic development. It leads to a gap or cleft in the center of the lip, the roof of the mouth (hard palate), or both. Often this condition leaves an open space through the roof of the mouth into the breathing passages. These conditions have a wide range in severity. Usually the upper lip and palate are affected; a cleft in the lower lip is rare. Most cases are inherited, although nutritional deficiencies during pregnancy, drug or chemical exposure, injury to the fetus, and some viral infections during pregnancy have also been suggested as causes.

Cleft palate or lip will usually be noticed shortly after birth when the foal might have problems with nursing. For example, milk might be seen dripping from the nostrils or the foal might have difficulty suckling and swallowing. The veterinarian can usually identify the problem by examining the foal’s mouth, although a cleft involving only the soft palate may be difficult to see. Affected foals require intensive nursing care, including hand or tube feeding and possibly antibiotics to treat secondary respiratory infections. Surgical correction is effective only in minor cases. The decision to perform surgery should be made carefully, and the affected animal should be neutered to prevent passing the defect on to future offspring.

Brachygnathia occurs when the lower jaw is shorter than the upper jaw. This condition is called “parrot mouth” in horses. It can be a minor problem or a serious defect depending on the degree of abnormality. Mild cases may cause no problems. More severe cases can cause damage to the hard palate (roof of the mouth) or restriction of normal jaw growth.

Prognathia occurs when the lower jaw is longer than the upper jaw. If a foal is badly affected, nursing may be impossible. Treatment consists of rasping or shearing the points and projections on the teeth that are causing difficulty.


In most animals, having too few teeth is rare. Extra teeth occur in some horses; these extra teeth are commonly found in the incisor and molar regions of the mouth. The result may be crowding and rotation of the teeth. Extra teeth are either removed or periodically rasped, especially if they interfere with chewing or are irritated by a bit.

Abnormalities in placement or shape of teeth sometimes occur. This may affect the incisors and result in rotation or overlapping of adjacent teeth. Usually, this does not cause any problems, but it may require extraction of some teeth if crowding or bite abnormalities occur.

Enamel defects such as disruption of tooth enamel formation may be caused by fever, trauma, malnutrition, poisoning, or infection. The damage can vary, depending on the severity and duration of the cause, from pitted enamel to the absence of enamel with incomplete tooth development. Affected teeth are prone to plaque and tartar accumulation and subsequent tooth decay.

Cysts of the Head and Neck

Cysts (lumps) in the head and neck can be caused by imperfections during fetal development. These need to be distinguished by your veterinarian from abscesses or lumps caused by infection or other disease. Dentigerous cysts arise from abnormal tooth development and often contain tooth fragments. These cysts can be found in horses less than 3 years of age, and they may be difficult to distinguish from cystic sinuses, another condition which can result in face or jaw distortion. Surgical removal of the cysts is required. The veterinarian can then make a final diagnosis based on examination of the removed tissue.

Some cysts arise from abnormal tooth development.


A hernia is the protrusion of a portion of an organ or tissue through an abnormal opening. One common congenital type, called a hiatal hernia, involves an abnormal opening in the wall of the diaphragm (the sheet of muscle that separates the chest from the abdomen) or the abdomen. The defect may allow abdominal organs to pass into the chest or bulge beneath the skin. Hernias may be congenital (present at birth) or result from injury. Signs of a hernia vary from none to severe and depend on the amount of herniated tissue and its effect on the organ involved.

Hernias involving the abdominal wall are called umbilical, inguinal, or scrotal, depending on their location (see Table: Types of Hernias). Diagnosis of umbilical hernias is usually simple, especially if the veterinarian is able to push the hernia back through the abdominal wall (called reducing the hernia). If not, the hernia must be differentiated from an umbilical abscess, which is common in horses. The veterinarian may need to use a fine needle to collect tissue or fluid for confirmation of the diagnosis. These hernias are corrected by surgery. The tendency to develop hernias may be inherited.

Inguinal hernias are sections of the intestine that break into the inguinal canal located in the groin. Inguinal hernias in colts often resolve spontaneously during the first year of life, so early corrective surgery is not recommended unless the hernia is strangulated or so large that it interferes with walking.


Besides hiatal hernias (see Congenital and Inherited Disorders of the Digestive System in Horses : Hernias), another abnormality involving the stomach is pyloric stenosis. It can be acquired or inherited, but the inherited form is rare in horses. Pyloric stenosis results from muscular thickening of the “exit” of the stomach (pyloric sphincter). This obstructs the flow of digested food from the stomach to the small intestine. Signs may include loss of appetite and other signs, such as abdominal pain, that are usually associated with colic. Treatment is through dietary modification and medication. In more severely affected cases, surgery may be beneficial.

Small and Large Intestine

Maldigestion is a condition in which certain foods are not properly digested. Malabsorption occurs when nutrients are not properly absorbed into the bloodstream. Both of these conditions often cause chronic, persistent digestive system problems including weight loss and diarrhea. Malabsorption and maldigestion are often treated with a combination of dietary changes and medication; the exact treatment will depend on the condition being treated.

A defect in the colonic nerves called ileocolonic agangliosis is seen in white foals produced by matings of Overo horses. Although the foals appear normal at birth, they soon develop colic and die on the second day. The affected horses are white and have blue irises. Diagnosis can be confirmed by the lack of specific nerves in the colon.

Congenital defects of the rectum and anus generally result from arrested embryonic development. Inherited closures (atresias) of the small- and large-intestinal tracts are relatively common in large animals and are always fatal. Atresia of the colon has been reported in Percheron horses. Segmental aplasia (also called rectal agenesis) is a condition in which the rectum is closed off before reaching the anus. Surgical correction is difficult because the location of the closure varies, and damage to nerves in the area may occur during surgery.


The most common congenital liver defect present at birth is a portosystemic shunt . In a healthy animal, blood coming from the intestines is processed by the liver, which removes toxins from the bloodstream before they reach the brain or other organs. In an animal with a portosystemic shunt, however, blood bypasses the liver through one or more “shortcuts” (shunts) and enters directly into the general circulatory system. Signs of a portosystemic shunt include nervous system disturbances and a failure to grow and thrive. In the late stages, protein-containing fluid may accumulate in the abdomen, a condition called ascites. Your veterinarian may also notice enlargement of the kidneys and kidney stones. A definite diagnosis is made by using an opaque dye to highlight the blood vessels, followed by x-rays. This procedure can identify the location of the shunt and determine whether it is single or multiple. It also allows the veterinarian to assess whether surgical correction is possible. Animals with multiple shunts tend to do poorly.

Other liver developmental anomalies include hepatic (liver) cysts, which generally cause no signs. They are significant mainly because they must be differentiated from abscesses in the liver. A veterinarian who finds a hepatic cyst will often want to examine the kidneys because hepatic cysts often occur along with polycystic kidney disease.

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