Purpose: Genetic variations in EGFR may alter protein function and therefore the therapeutic efficacy of epidermal growth factor receptor inhibitors. This study investigated the association between polymorphisms in EGFR and clinical outcome in patients with advanced non-small-cell lung cancer (NSCLC) treated with Gefitinib. Methods: A whole gene-based tag-SNP approach was used to determine the candidate SNPs in EGFR. Four tag SNPs, one CA simple sequence repeat (CA-SSR) in intron 1, one coding region SNP (R521K), and SNPs identified by resequencing in the tyrosine kinase domain of EGFR were selected to analyze their association with therapeutic outcome and survival in 84 advanced NSCLC patients treated with Gefitinib. Progression-free and overall survivals were computed by Cox model adjusted for clinical factors. Results: We identified two EGFR polymorphisms, rs2293347 (D994D) and CA-SSR in intron 1, associated with clinical outcome of Gefitinib therapy. The response rate for the rs2293347GG or shorter CA repeat genotype was significantly higher than that for the rs2293347GA or AA or longer CA repeat genotype (71.2% versus 37.5%, P = 0.0043 and 88.5% versus 48.3%, P = 0.0005). The rs2293347GG genotype was also associated with longer progression-free survival compared with the rs2293347GA or AA genotype (11 months versus 3 months, P = 0.0018). A combination of rs2293347GG and shorter CA repeat genotypes had more pronounced clinical benefit. Conclusion: The D994D and CA-SSR polymorphisms in EGFR are potential predictors for clinical outcome in advanced NSCLC patients treated with Gefitinib. © 2009 Elsevier Ireland Ltd. All rights reserved.