Bronchioloalveolar carcinoma (BAC) is classified as a subset of lung adenocarcinoma but has a distinct clinical presentation, tumor biology, response to therapy, and prognosis compared with other subtypes of lung adenocarcinoma. This study was designed to investigate the clinicopathological differences between BAC and adenocarcinoma and the expression of focal adhesion kinase (FAK) and phosphatase and tensin homologue (PTEN) and their clinical significance in BAC and adenocarcinoma. A retrospective analysis was performed on 77 patients with BAC and 172 patients with pure adenocarcinoma seen during the period from January 1998 to December 2000. All patients underwent lobectomy or pneumonectomy and systematic lymph node dissection. Paraffin-embedded tissue blocks from these patients were obtained and expressions of PTEN and FAK were evaluated by using immunohistochemical staining. Clinicopathological characteristics and survival outcome were reviewed and compared between patients with BAC and adenocarcinoma. Lymph node status, clinical symptoms, CT appearance and expression of FAK were different between BAC and adenocarcinoma. The overall survival of BAC was better than that of adenocarcinoma. In patients with FAK(-), the overall survival was not different between BAC and adenocarcinoma. In patients with adenocarcinoma, the overall survival was better for FAK(-) compared with FAK(+). Expression of PTEN had a prognostic significance in patients with BAC and adenocarcinoma. BAC and adenocarcinoma have different clinicopathological presentations. Expression of FAK has some effect on such differences and affects survival of lung adenocarcinoma. Expression of PTEN can predict outcome of resected lung adenocarcinoma and BAC.