The prognosis of lung cancer patients treated with chemotherapy is poor, motivating the search for predictive factors. Single nucleotide polymorphisms (SNPs) in membrane transporter genes could influence the pharmacokinetics of cytostatic drugs and therefore affect treatment outcome. We examined 6 SNPs with known or suspected phenotypic effect: ABCG2 G34A, C421A; ABCC3 C2211T, G3890A, C3942T and CNT1 G565A. For 349 Caucasian patients with primary lung cancer [161 small cell lung cancer (SCLC), 187 nonsmall cell lung cancer (NSCLC) and 1 mixed] receiving first-line chemotherapy 3 different endpoints were analyzed: response after the 2nd cycle (R), progression-free survival (PFS) and overall survival (OS). The prognostic value of the SNPs was analyzed using multivariable logistic regression, calculating odds ratios (ORs) when comparing genotype frequencies in responders and nonresponders after the 2nd cycle. Hazard ratios (HRs) for PFS and for OS were calculated using Cox regression methods. In all lung cancer patients, none of the investigated polymorphisms modified response statistically significant. The only significant result in the histological subpopulations was in SCLC patients carrying the ABCC3 -211T allele who showed significantly worsened PFS (HR: 1.79; 95% confidence interval (CI) 1.13-2.82).In an exploratory subgroup analysis significantly worse OS was seen for carriers of the ABCG2 421A-allele treated with platinumbased drugs (HR: 1.60; 95% CI 1.04-2.47; n 5 256). In conclusion, this study prioritizes ABCC3 C-211T and ABCG2 C421A as candidate transporter SNPs to be further investigated as possible predictors of the clinical outcome of chemotherapy in lung cancer patients. ' 2008 Wiley-Liss, Inc.Key words: lung neoplasms; multidrug resistance-associated proteins; ABCC3, ABCG2, CNT1; pharmacogenetics Despite various improvements in the treatment of lung cancer the overall prognosis remains poor: In Germany the 5-year survival rate is 12% for men and 14% for women. 1 Patients can be treated by surgery, radiation and chemotherapy alone or in combination, using standard treatment protocols. 2 Nonsmall cell lung cancer (NSCLC) patients with localized tumors are mostly treated surgically while nonlocalized NSCLC is primarily treated with radiotherapy. Small cell lung cancer (SCLC) is mostly treated by chemotherapy with or without radiotherapy. In Europe between 1980 and 1997, the fraction of patients receiving chemotherapy has increased, especially of patients at a later tumor stage. 3 Even in patients that are comparable regarding histology, tumor stage and age there is great variation in the response to chemotherapy. 4,5 In part, this is due to genetic diversity caused by single nucleotide polymorphisms (SNPs) in genes involved in the metabolism and transport of chemotherapeutic drugs. In NSCLC patients treated with irinotecan and cisplatin, the UGT1A1 genotype significantly influenced the pharmacokinetics of the drugs, progressionfree survival (PFS) and overall survival (OS). 6 Sohn et al. 7 showed that...