Gene expression profiles of resected tumors may predict treatment response and outcome. We hypothesized that profiles derived from lung tumor biopsies would discriminate tumor-specific gene signatures and provide predictive information about outcome. Lung carcinoma specimens were obtained from 23 patients undergoing computed tomography-guided transthoracic biopsy or endobronchial brushing for undiagnosed nodules. Excess tissue was processed for gene profiling. We built class prediction models for lung cancer histology and for cancer outcome. The histology model used an F test to identify 99 genes that were differentially expressed among lung cancer subtypes. The histology validation set class prediction accuracy rate was 86%. The outcome model used the maximum difference subset algorithm to identify 42 genes associated with high risk for cancer death. The outcome training set class prediction accuracy rate was 87%. In conclusion, gene expression profiles of biopsy specimens of lung cancers identify unique tumoral signatures that provide information about tissue morphology and prognosis. The use of specimens acquired from lung biopsy procedures to identify biomarkers of clinical outcome may have application in the management of patients with lung cancer. The procedures are safe and feasible; the efficacy and utility of this strategy will ultimately be determined by prospective clinical trials.