Gastrointestinal Cytology – Introduction

Latha Pisharodi, MD

The Gastrointestinal (GI) tract or the gut is divided into the esophagus, stomach, small intestine and large intestine. They are separated by sphincters that control the passage of contents from one part of the GI tract to the next. In addition, each of these divisions is characterized by a change in the mucosal nature of the lining cells. The GI tract is the digestive organ for the body, a source of immunity generation and an endocrine organ.

Specimen Collection

Cytologic specimens obtained from the GI tract may be brushings, washings, or Fine Needle Aspiration Biopsies (FNA) under ultrasound guidance. A brushing specimen is usually obtained by passing a brush enclosed inside a transparent sheath through the endoscope and plunging the brush into the lesion five to ten times. The brush is then retracted and the specimen is extruded onto glass slides or into a preservative medium.

The endoscopic FNA involves introducing the needle through a fiberoptic endoscope. When the lesion is localized, negative pressure is applied to the needle and the needle is moved back and forth within the lesion. The pressure is released, the needle is withdrawn and the specimen is collected into a preservative solution.

The specimens may be collected into CytoLyt® Solution and processed using the ThinPrep® 2000 processor or collected into other preservative solutions and processed as cytospins or traditional smears.


Normal lining cells of the esophagus consist of non-keratinized squamous epithelial cells. Rarely, metaplastic cells derived from submucosal glands may be seen. Columnar glandular cells may be derived from the stomach, or from Barrett’s esophagus.

Non-specific esophagitis usually shows acute and/or chronic inflammation with reactive changes. Herpetic esophagitis shows classic cytopathic effects consisting of multinucleation, eosinophilic viral inclusions and ground glass nuclei. Candidal esophagitis is diagnosed by the detection of fungal spores and pseudoseptate hyphae. Rarely, other organisms like Aspergillus may be observed.

Cytologic evaluation of the esophagus is an important tool in the diagnosis of esophageal carcinoma, especially in countries with a high incidence of esophageal cancer such as China and Japan, where it is used as a mass screening program. Several authors have showed that a combined cytology -biopsy approach is the most preferred technique for the diagnosis of upper GI neoplasms 1, 2. Glandular dysplasia arising in a background of Barrett’s esophagus typically shows scattered atypical cells with some, but not all, features of adenocarcinoma. Atypical squamous cells with bizarre shapes, hyperchromasia and pleomorphism characterize well-differentiated squamous cell carcinomas. Poorly differentiated squamous cell carcinomas usually show highly pleomorphic cells with high N; C ratio, nucleoli and dense cytoplasm. Adenocarcinomas typically show groups and clusters of neoplastic epithelial cells.


The lining epithelium of the stomach consists of columnar glandular cells usually arranged in honeycomb sheets. Mucin vacuoles may be observed. Parietal and chief cells are rarely seen in gastric brushings. Parietal cells have acidophilic cytoplasm with the pap stain. Chief cells are best identified by Romanowsky stain 3. Helicobacter pylori are gram-negative spiral bacteria easily identified on Pap, Romanowsky, Warthin-Starry and H & E stains. Non-specific reactive and reparative changes, inflammatory cells, mitotic activity, and prominent nucleoli characterize peptic ulcer disease and gastritis. Gastric adenocarcinomas show malignant epithelial cells with pronounced atypia. Signet ring cells may be present. Malignant squamous cells, if present, suggest either adenosquamous carcinoma, the rare pure squamous carcinoma of the stomach or extension of esophageal squamous cell carcinoma into the stomach. Other tumors such as carcinoid and stromal tumors may be rarely diagnosed by gastric brush cytology. However diagnostic sensitivity of these tumors by cytology is far higher by using endoscopic FNA procedure rather than brushing.

Bile Duct

Biliary tract brushings are usually acquired through endoscopic retrograde cholangiopancreatography (ERCP). Specimens can also be obtained from biliary stents. The main indication for biliary cytology is suspected malignancy in a patient with a biliary stricture. Reactive and reparative changes are frequently seen with infectious diseases, and primary sclerosing cholangitis (PSC). Dysplasia may be observed in the biliary tract. Cytologic features include crowding and overlapping, increased nuclear to cytoplasmic ratio and abnormal chromatin distribution. The atypia, however, is less severe than in adenocarcinoma. Adenocarcinoma in the biliary tract (cholangiocarcinoma) is cytologically similar to those seen in the GI tract. The mucinous variant can be especially difficult to diagnose due to its bland cytologic features. These cells contain abundant mucin and can be sometimes mistaken for histiocytes.


Cells may be obtained by endoscopic brushing, washing or by FNA. Normal colonic mucosa is represented by tall columnar cells arranged in sheets or singly. Goblet cells may be seen. Some authors have described cytologic findings of adenoma wherein tubular adenoma has more flat and blunted cells while villous adenoma has elongated and spindly cells 4. Adenocarcinoma of the colon shows cohesive, highly atypical groups of glandular cells with prominent nucleoli and a necrotic background. The sensitivity of colonic brushing in the diagnosis of colon carcinoma ranges from 70 to 85 % 5. Combining cytology with biopsy however, yielded best accuracy 6.

Anal Brushings

Much like the transformation zone of the cervix, the squamocolumnar junction of the anal canal is prone to the development of neoplasia 7. The cytologic appearance of the two sample types is very similar. In fact, findings may be classified according to the criteria defined by the Bethesda System 8.
Cytologic material for evaluation is easily obtained by directly scraping the area and smearing it on glass slides or rinsing into a preservative. In addition, anal “pap” smears are being increasingly employed as a screening tool to assess dysplastic changes, especially in the HIV positive population 9. Squamous cell carcinomas of the anal region show characteristic neoplastic squamous cells with varying degrees of differentiation.


  1. C P Shroff, S A Nanivadekar: Endoscopic brushing cytology and biopsy in the diagnosis of upper gastrointestinal tract lesions. A study of 350 cases. Acta Cytol 1988: 32 (4}: 455-60.
  2. O Donoghue, P G Horgan, M K Donohoe et al: Adjunctive endoscopic brush cytology in the detection of upper gastrointestinal malignancy. Acta Cytol 1995: 39(1}: 28-33.
  3. M Drake: Gastric cytology: normal and abnormal. In Gastroesophageal Cytology. Basel: Karger, 1985, page 120.
  4. V Kannan, CB Masters: Cytodiagnosis of colonic adenoma: morphology and clinical importance. Diag Cytopathol 1991 7(4}: 13-16
  5. RG Bardawil, FG Ambrosio, SI Hajdu: Colonic cytology. A retrospective study with histologic correlation. Acta Cytol 1990; 34 (5}: 10-12
  6. M Halpern, R Gal, L Rath-Wolfson, R Koren et al. Brush cytology and biopsy in the diagnosis of colorectal cancer. A comparison. Acta Cytol 1997; 41 (3}: 628-32.
  7. Goldstone et al. High Prevalence of Anal Squamous Intraepithelial Lesions and Squamous Cell Carcinoma in Men Who Have Sex with Men as Seen in a Surgical Practice. Dis Colon Rectum 2001;44:690-698.
  8. Darragh et al. Comparison of Conventional Cytologic Smears and ThinPrep Preparations from the Anal Canal. Acta Cytol 1997;41:1167-70.
  9. MA Friedlander, E Stier, O Lin. Anorectal cytology as a screening tool for anal squamous lesions: cytologic, anoscopic, and histologic correlation. Cancer 2004: 102(1}:19-26.

Esophageal Cytology