An endoscopy uses a flexible tube equipped with a light and a camera (endoscope) to visually examine the lining of the digestive tract. Physicians often simultaneously take a biopsy, collecting a small tissue sample. This combination of direct visualization and cellular analysis provides the most comprehensive diagnostic information for conditions affecting the esophagus, stomach, and intestines.
Why Visualization Alone Is Not Enough
The endoscope offers a high-definition, macroscopic view of the mucosal surface, revealing details about color, texture, and structure. However, the human eye cannot determine the nature of the cells that make up the tissue, which is the limitation of visualization alone. A visual assessment can only suggest a diagnosis based on patterns of inflammation or growth. Definitive diagnosis requires a microscopic examination of the tissue structure and the individual cells within it.
The purpose of the biopsy is to determine the cellular identity of any change, answering whether the tissue is benign, precancerous, or malignant. For instance, two lesions may appear identical, but one may be a harmless scar while the other is an early-stage tumor. Only the pathologist, by analyzing the sample under a microscope, can assess the architecture of the cells and confirm the presence or absence of disease. This distinction between a visual suspicion and a confirmed cellular diagnosis is important for selecting the correct treatment plan.
Investigating Visible Abnormalities
A targeted biopsy is performed immediately when the physician observes an abnormal area, ensuring the sample comes directly from the suspicious site. One common finding is a polyp, an abnormal growth of tissue protruding from the lining of the digestive tract. While many polyps are harmless, only microscopic analysis can identify if the cells show low-grade or high-grade dysplasia, markers for precancerous change. The removal and analysis of these growths are a major preventative measure against cancer.
Biopsies are also taken from ulcers and erosions, which are open sores or breaks in the mucosal lining. The goal is to identify the underlying cause, such as severe inflammation, an infection like Cytomegalovirus, or a possible malignancy masquerading as an ulcer. Similarly, if the physician notes a stricture (a narrowing of the tract) or a visible mass, a biopsy is necessary to characterize the cell type and confirm if the narrowing is due to scar tissue or a tumor pressing on the wall.
Tissue color or texture changes also warrant sampling, notably in the esophagus, where Barrett’s Esophagus can develop. This condition involves the replacement of the normal squamous cells with columnar cells, similar to those found in the intestine. This change is associated with an increased risk of esophageal adenocarcinoma, and repeat biopsies are the only reliable way to monitor these cellular changes for signs of progression. Sampling the abnormal area provides a precise cellular profile that guides the decision for ongoing surveillance or immediate intervention.
Diagnosing Conditions That May Not Be Visible
A biopsy is often necessary to diagnose conditions even when the digestive tract appears normal or only mildly inflamed. For example, Celiac Disease is an autoimmune disorder that requires tissue samples from the small intestine to confirm the diagnosis. The pathologist specifically looks for signs of villous atrophy—the flattening or blunting of the small, finger-like projections (villi) responsible for nutrient absorption. This microscopic damage is frequently not severe enough to be obvious during the visual examination.
Inflammatory Bowel Diseases (IBD) like Crohn’s Disease or Ulcerative Colitis are often confirmed through biopsy, especially in cases of Microscopic Colitis. In this form of IBD, the colon lining may appear healthy to the endoscopist. However, a pathologist examining the tissue will observe specific patterns of inflammation, such as an increased number of lymphocytes or plasma cells within the lamina propria layer. These cellular details help differentiate IBD from other non-inflammatory gastrointestinal issues.
Infections also necessitate tissue sampling for definitive identification, such as the bacterium Helicobacter pylori (H. pylori), a common cause of gastritis and ulcers. While a rapid urease test can be performed on a biopsy sample during the procedure, a portion of the tissue is often sent to the lab. The pathologist can stain the sample to visualize the spiral-shaped bacteria directly on the mucosal surface, confirming the infection in a way not possible through visualization alone.
The Path of the Sample
Once the tissue is collected using specialized forceps, it is immediately placed into a container filled with a preservative solution, typically 10% neutral buffered formalin. This chemical fixative stops all cellular processes, “freezing” the tissue in time to prevent degradation and maintain its structure. The container is labeled with the patient’s information and the exact site from which the sample was taken, such as “gastric antrum” or “cecum.”
The fixed sample is then transported to the pathology laboratory where the pathologist takes over the analysis. Technicians process the tissue by embedding it in a block of paraffin wax, which hardens to provide a solid medium for slicing. Extremely thin sections (often only a few micrometers thick) are cut from the block and mounted onto glass slides. These slices are then stained with chemical dyes, like Hematoxylin and Eosin (H&E), to make the cellular components visible under the microscope.
The pathologist examines these slides to assess the cellular architecture, looking for abnormal cell shapes, nuclear changes, or infiltration by inflammatory cells. After review, they generate a detailed report containing the final diagnosis, which is then sent to the referring physician. Results are typically available within a few days to a week, depending on the complexity of the required tests.