Basic Cytology of the Avian Gastrointestinal Tract

Key Points

  • Cytologic evaluation of the oropharynx is indicated when plaques, nodules or ulcers are identified during physical examination.
  • Vitamin A deficiency causes hyperkeratosis and hyperplasia of squamous epithelium and squamous metaplasia of non-squamous epithelium. Cytology reveals large numbers of squamous epithelial cells and small tissue fragments composed of tightly packed squamous epithelial cells. Basophilic staining is associated with keratinization.
  • Cytological evaluation of the crop, or ingluvies, is indicated when vomiting, frequent regurgitation (non-reproductive behavior), or delayed crop emptying is observed.
  • Candidiasis is characterized by a large number of oval, thin-walled, narrow-based budding yeasts that typically stain deeply basophilic.
  • Cloacal cytology is indicated in patients with cloacal inflammation, cloacal prolapse, and/or cloacal mass lesions.
  • Fecal cytology can be a useful test in patients suffering from anorexia or signs of gastrointestinal upset such as diarrhea, vomiting, or regurgitation.
  • Abnormal findings in cloacal or fecal swabs include heterophilic inflammation and/or the presence of monomorphic microbial populations, large numbers of yeasts (narrow-based budding forms and/or those with hyphae formation), and protozoa.
  • The gastrointestinal flora of psittacines and other granivorous birds consists primarily Gram-positive bacteria, although it is not uncommon to find the occasional Gram-negative bacteria in parrot digestive tracts. Songbirds also tend to have Gram-positive bacteria; however, their numbers are normally quite scant.
  • Species that employ other digestive strategies, such as birds of prey or fowl, normally possess large numbers of Gram-negative bacteria.

Historically, routine Gram’s stains were performed in apparently healthy birds. As our understanding of avian medicine has grown, avian veterinarians have questioned the reliability and validity of Gram’s stain cytology as a screening test. Cytology is indicated when specific problems are reported during a detailed medical history or when . . .

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Campbell TW, Ellis CK. Avian and Exotic Animal Hematology and Cytology. Ames, Iowa; Blackwell Publishing; 2007. Pp. 169-180.

Fischer I, Christen C, Lutz H, et al. Effects of two diets on the haematology, plasma chemistry and intestinal flora of budgerigars (Melopsittacus undulatus). Vet Rec 159(15):480-484, 2006.

Hannafusa Y, Bradley A, Tomaszewski EE, et al. Growth and metabolic characterization of Macrorhabdus ornithogaster. J Vet Diagn Invest 19:256-265, 2007.

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Son TT, Wilson GH, Latimer KS. Clinical and pathological features of megabacteriosis (Macrorhabdus ornithogaster) in birds. Updated September 23, 2004. Available at Accessed April 28, 2012.

To cite this page:

Campbell T. Basic cytology of the avian gastrointestinal tract. April 28, 2012. LafeberVet Web site. Available at