BACKGROUND: Diagnostic bronchial biopsy samples from lung cancer patients may be used for molecular biologic analyses to help select therapy and provide prognostic information. Some have suggested that direct molecular analysis of bronchial biopsy fragments may be feasible, bypassing histologic examination. We analyzed a series of 100 bronchial biopsy specimens in lung cancer patients to assess the frequency and quantity of tumor present in biopsy samples. METHODS: The proportion of tumor in bronchial biopsy specimens was assessed by measuring the tumor area in histologic sections using computer-aided morphometry. RESULTS: In only 48% of cases did all the biopsy fragments contain some tumor. The median number of fragments obtained at bronchoscopy was 4; median number actually containing tumor was 3. The mean total surface area of tumor (as a percentage of the total sample area) in biopsy fragments was, for all cases, 33.4%; median area 28%. Biopsies with small cell carcinoma had more tumor (mean area 46.5%, median 49%; p = 0.0006) than all other non-small cell carcinoma cases. CONCLUSION: Malignant bronchial biopsy samples frequently contain limited amounts of primary carcinoma. Often, one or more of the biopsy fragments will not contain tumor. This has important implications for the storage and use of bronchial biopsy samples for genetic analysis.