Lung cancer is the most common malignant disease leading to death worldwide. Histologically, it is broadly subcategorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), with the latter mainly consisting of the major entities adenocarcinoma and squamous cell carcinoma. However, molecular profiling of various lung cancer entities has revealed major molecular differences within distinct histological tumor entities, resulting in the integration of molecular alterations in the subclassification of lung cancers. These findings can only estimate the genetic complexity of lung tumors. Large scale molecular profiling has the potential to identify novel diagnostic, prognostic and predictive markers as well as therapeutic targets. Importantly, this recently arising categorization of lung carcinomas can be regarded as an example for the characterization of malignomas of other organ systems. The pioneer model for this molecular subcategorization is the classification of malignant lymphomas.