We present here new molecular tools such as gene expression microarrays as promising biomarkers for diagnosis and prognosis in lung cancer as well as for an early diagnosis of malignancy after lung transplantation. Data regarding gender differences in survival, recently collected in a single-institution study, may allow better targeting of immunosuppression goals to maintain effectiveness while minimizing cancer development and progression. Combining these differing types of data using an integrative approach that is the central theme of systems biology may allow us to provide powerful and more individualized risks of cancer after lung transplantation.