Standard first-line treatment for advanced-stage non-small cell lung cancer (NSCLC) usually consists of platinum-based doublet chemotherapy, but progression ultimately occurs for most patients. Second-line treatment options available to patients who suffer failure of first-line treatment include further chemotherapy (docetaxel and pemetrexed) or targeted therapy. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) show great efficacy in patients with advanced NSCLC with EGFR mutation. High EGFR gene copy number was associated with great sensitivity and prolonged progression-free survival of NSCLC from EGFR-TKIs. This phase II study was designed to assess the efficacy and safety of erlotinib compared with pemetrexed as second-line treatment for EGFR wild-type and EGFR FISH-positive lung adenocarcinoma.