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Avian gastrointestinal anatomy and diseases (Proceedings)


Gastrointestinal diseases and disorders are common in avian patients. This presentation will give an overview of anatomy and clinical presentations of gastrointestinal (GI) disease in birds.

Gastrointestinal diseases and disorders are common in avian patients.This presentation will give an overview of anatomy and clinical presentations of gastrointestinal (GI) disease in birds.


The avian gastrointestinal tract (GIT) consists of the oral cavity, esophagus, ingluvies (crop), proventriculus, ventriculus, small and large intestine, and cloaca.

Diagnostic Techniques

Numerous diagnostic techniques are available for the diagnosis of GIT disease. The order of testing is based on signalment, physical exam findings and clinical signs. Consideration of species predilection for certain diseases can be helpful when developing a diagnostic plan. The history should include exposure to infectious diseases, diet, environment/housing, reproductive history, administration of medication and management practices. Critically ill birds should be stabilized prior to performing stressful diagnostic tests. Staging of diagnostic tests is often necessary for the patient. Anesthesia may be required for diagnostic testing such as radiography. Diagnostic tests useful for the evaluation of gastrointestinal disorders include a gram's stain of a crop swab or feces, parasite analysis, hematology, biochemistries, electrolytes, cytology, protein electrophoresis, microbiology, Chlamydophila testing, lead and zinc blood levels, viral testing, acid fast stain, radiography, endoscopy, biopsy, or necropsy.

Oral Cavity

The oropharynx is common site for variety of lesions. A thorough examination may not be entirely possible in the awake patient. A quick visual examination can be performed in most birds. Clinical signs of oropharyngeal disease include halitosis, anorexia, inappetence, dysphagia, rubbing of the beak or face, gaping, oral lesions such as plaques or granulomas. Differentials for oral plaques include bacterial infection, yeast/fungal infection, hypovitaminosis A, parasitic (trichomoniasis), or viral (pox). Cytology and/or culture of the lesion will help to determine the etiology. Cytological samples may be collected by rubbing a sterile cotton-tipped applicator along the lesion. This sample can then be placed on a clean glass slide. Samples for culture can be placed into proper culture media tubes for processing. Fresh preparations are good for looking for parasites (wet mount).

Bacterial Infections of Oropharynx

Pathogenic bacteria can cause granulomas or generalized stomatitis. Examples of bacterial organisms involved in infection include Staphylococcus sp., Klebsiella sp., gram-negative bacteria. Bacterial overgrowth may be caused by underlying immunosuppressive diseases or may be secondary to damage to the oral mucosa by irritants, rough food items, or accumulation of food caused by beak deformities. Treatment may include topical or systemic antibiotic therapy based on culture and sensitivity results. Topical treatment may be performed by placing an antiseptic solution such as chlorhexidine (1 ml in 30 ml of water) in the water supply or by gently flushing the oral cavity.


Granulomas can also be caused by Mycobacteria sp. Mycobacterium avium is the most commonly isolated species from oral lesions in birds. M. genovense and M. tuberculosis have also been identified. Mycobacteriosis more commonly affects the lower GIT.


Candida infection causes white plaques within the oral cavity. Candida albicans is most frequently cultured. Infection may be primary or secondary to other systemic or oropharyngeal disease or long term antibiotic usage. This disease is called "thrush" by falconers. Cytology of the lesion reveals darkly staining budding yeast cells. Treatment may be topical with chlorhexidine or nystatin (300,000 IU/kg PO BID) for mild infections (non-systemic). In order for topical treatment to be effective the medication much come into contact with the lesion. Severe or systemic infections may require systemic antifungal such as ketoconazole, itraconazole or fluconazole.

Hypovitaminosis A

Vitamin A deficiency can result in squamous metaplasia of the epithelial lining of the oral cavity. Formation of plaques or granulomas can also occur. The choana may be wider than normal or papillae may be blunted. Cytology of lesions will often show only scant normal Gram positive bacteria. Granulomas can become secondarily infected. Biopsy of the lesion aids in diagnosis. Dietary history of diet deficient in Vitamin A can provide presumptive diagnosis.

Treatment involves dietary correction. Parenteral Vitamin A can be given for one or two doses which diet is being corrected. The choana and choanal papillae may remain abnormal even after treatment.

Parasitic Diseases of Oral Cavity

A wide variety of parasitic diseases may cause oral lesions in the avian patient. Examples are Capillaria sp. and trichomoniasis.

Pox Virus Infection

Insect vector is involved in transmission. Diagnosis is made from biopsy and histopathology. Treatment includes supportive care only and limiting vector exposure.

Traumatic Injury to the Tongue

Like mammals, the tongue of birds is very vascular and may bleed extensively when injured. Injury from prey for carnivores, burns, laceration and foreign bodies can occur.

Treatment involves repair of the wounds and prevention of secondary infection. Some birds may require nutritional support in severe cases (pharyngostomy tube).


Neoplasia of the oral cavity is uncommon in the avian patient. Types of oral neoplasia documented in birds include sqaumous cell carcinoma, papillomas, fibrohistiosarcoma, and fibrosarcomas.

Esophagus and Crop

Many diseases that affect the oral cavity also affect the esophagus and crop such as bacterial infections, candidiasis, trichomoniasis, capillariasis.

Clinical Signs of Crop or Esophageal Disease

Clinical signs can include regurgitation, inappetence, anorexia, delayed crop emptying, metabolic or systemic disease. Crop stasis or "sour crop" is term used to describe lack of normal crop motility and emptying. Crop stasis is not specific to one disease process. Crop stasis can be primary or secondary to systemic disease. The normal flora of the crop in most species includes few gram-positive bacteria, scant, non-budding yeast. Gram negatives should not be present or in appropriate numbers with carnivorous species. Overgrowth of gram positives or gram negative organisms can occur as primary or secondary problem.

Diagnosis of Crop Disorder

Cytology of the crop via aspirate or crop swab often provides quality information. A bacterial culture and sensitivity is usually recommended. Radiographs or other imaging can be useful. Surgical biopsy of crop tissue is often necessary for definitive diagnosis with viral disease such as Proventricular Dilatation Disease (PDD).

Candidiasis (Candida albicans) infection of the crop is common in young birds due to undeveloped immune systems. Candidiasis can be a primary or secondary disease which often occurs simultaneously with bacterial overgrowth or antibiotic therapy. Diagnosis is made by identifying the presence of budding yeast spores on cytology. The presence of pseudohyphae indicates tissue invasion. Systemic infections are possible. A thickened crop wall with a "turkish towel" feel may occur. Treatment for candidiasis of the crop includes regular crop flushes, oral nystatin (must come into contact with the yeast) or systemic antifungals indicated with invasive or systemic infection.

Noninfectious Conditions of the Crop and Esophagus

Crop fistulas

Traumatic injuries

Foreign bodies

Neoplastic disease

Crop Fistulas

Crop wall can be damaged by hot food such as feeding formulas, table foods, hot beverages, microwaved foods with "hot spots". This condition is common in neonatal birds syringe or hand fed with microwaved formula. If the crop wall is burned, the tissue becomes necrotic. A fistulous tract will develop through the crop wall and skin. The clinician must allow enough time (few days) for the damaged tissue to declare itself prior to surgical correction. If there is subcutaneous deposit of food then the wound needs to be treated immediately.


Neoplasia of the crop and esophagous includes squamous cell carcinoma, adenocarcinoma, leiomyosarcoma, and fibrosarcoma. Clinical signs include dysphagia, regurgitation, anorexia, or inappetence. Diagnosis can be made from contrast radiographs, fluoroscopy, endoscopy,and/or biopsy with histopathology. An approach through the oral cavity to the esophagus or an ingluviotomy incision will allow access to the crop or esophagus. Treatment is often unrewarding and involves supportive care. Chemotherapy or radiation therapy options for the avian patient are limited at this time.

Proventriculus and Ventriculus

Macrorhabdosis (Megabacteriosis)

Macrorhabdosis is a disease of the proventriculus and ventriculus. The organism involved is a fungal organism recently named Macrorhabdus ornithogaster. This infection can be a primary or secondary disorder. There is discussion in the literature as to whether the organism is normal flora in some species. The fungal organism is 3-4 µm wide and 20-80 µm in length, rod shaped, Gram and PAS positive. This condition is called "going light" syndrome in small psittacines. There is high morbidity but low mortality. Findings include thickening of the proventricular wall, an increase in pH in the ventriculus which can lead to sloughing of the koilin layer. Diagnosis involves the demonstration of the organism in fecal samples or proventricular wash. Treatment includes acidification of water with acetic or citric acid, oral supplementation with Lactobacillus organisms (probiotic), and oral antifungal therapy with Amphoteracin B for at least 30 days duration.

Bacterial Proventriculitis

Bacterial proventriculitis is a primary or secondary problem. Gram negatives: E. coli, Klebsiella, Salmonella, Enterobacter spp. If infection extends to small intestinal tract can see clinical signs of diarrhea, maldigestion, malabsorption, anorexia, weight loss.

Foreign Bodies

Foreign materials ingested by birds include wood, metal, plastic, and bedding such as shavings, corncob, shredded paper, kitty litter. Ingestion can cause impactions or obstruction of the gastrointestinal tract. Ingestable bedding should not be used with neonates unless they can be closely monitored. Diagnosis is made via radiography, endoscopy, or exploratory surgery. Medical therapy should be tried first prior to surgery (flush crop, laxatives) unless complete obstruction is of concern. Some foreign bodies may be retrieved within endoscope if within the proventriculus or ventriculus. A pro/ventriculotomy may be required in some cases.

Ulcerative Lesions

Ulcerative lesions may be associated with foreign bodies, infectious disease, chronic stress. Ulcers can occur anywhere within the GI tract but are more common in proventriculus, isthmus or ventriculus.

Neoplasia of Proventriculus & Ventriculus

Neoplasia tends to occur at the isthmus between the proventriculus and ventriculus. Clinical signs: weight loss, anorexia, melena, maldigestion. Types of neoplasia include adenocarcinomas, carcinomas, leiomyosarcomas. Clinical signs include weight loss, anorexia, maldigestion, melena and/or voluminous droppings.

Intestinal Tract

Other intestinal tract diseases include bacterial enteritis, mycobacteriosis, protozoal infection, parasitic infections, heavy metal toxicosis, pancreatitis, or hepatic disease.


The cloaca is the common terminal structure to three body systems: the gastrointestinal tract, reproductive tract, and urinary system. The reader is referred to the author's presentation on cloacal diseases and disorders for further information.


Gastrointestinal diseases and disorders are common in companion avian species. Infection is one of most common etiologies for gastrointestinal disorders. Infection, either bacterial or fungal, can occur (primary or secondary). Distally, cloacal obstruction, including egg binding and cloacal prolapse, are a frequent causes of distal disease. Primary neoplasia of the avian gastrointestinal tract is an infrequent diagnosis in the avian patient.

Suggested Reading

Ritzman TK (Ed). Gastroenterology. Veterinary Clinics of North America, Exotic Animal Practice. W. B. Saunders Co. Philadelphia, PA, May 2005.

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