Current options for the second-line treatment of non-small cell lung cancer (NSCLC) include cytotoxic drugs, such as docetaxel and pemetrexed, and targeted therapies. Docetaxel was approved in the United States and Europe in 2000 after two phase III trials showed drug superiority versus best supportive care alone and versus alternative single-agent chemotherapy. Pemetrexed was approved in the United States and Europe in 2004 after a phase III trial showed that, compared with docetaxel, it had comparable activity (median survival time of approximately 8 months in both arms) and a more favorable toxicity profile: grade 3-4 neutropenia was observed in 5.3% versus 40.2% of patients in the pemetrexed and docetaxel arms, respectively, while febrile neutropenia was observed in 1.9% versus 12.7% of patients, respectively. In the United States, gefitinib and erlotinib have also been approved for the treatment of recurrent NSCLC (in 2003 and 2004, respectively), while in Europe the registration of these agents is currently under evaluation. This review focuses on the use of docetaxel and pemetrexed for the second-line treatment of NSCLC and compares these drugs with targeted therapies, highlighting the latest developments in pharmacogenomics that might lead to a more tailored approach to treatment.