Background Lung cancer is the leading cause of cancer-related death globally. Chemotherapy and targeted drugs increase progression-free survival, overall survival, and quality of life. Recently, we are moving towards personalised medicine based on genotypic study of enzymes involved in the metabolism, transport, and elimination of drugs routinely used in lung cancer. Methods After obtaining written informed consent, we analysed venous blood draws from 40 patients with NSCLC of all stages, before the start of chemotherapy. We studied polymorphisms, with real-time PCR, in genes involved in detoxification (GSTP1), DNA repair (XRCC1, ERCC1) in trans-membrane transport (ABCB1), and metabolism of anticancer agents (CYP2C9, CYP3A4, CYP3A5, CYP2D6, CYP1A2, UGT1A1, TSER). Findings We are prospectively analysing the correlation between polymorphisms and toxicity of chemotherapy regimens and progression-free survival, overall survival, and quality of life. We expect a greater toxicity in patients with polymorphisms that result in reduced activity of enzymes involved in drugs metabolism, a reduction in transport, and in DNA repair activity. Interpretation Considering that there is no standard first-line chemotherapy for NSCLC, since platinum-based regimens are equally effective, the toxicity of each regimens affects choice of treatment. Therefore, the objective of this study is to identify factors that can direct choice of chemotherapy regimen based on the patient’s genotype.