Recent advances in non-small-cell lung cancer (NSCLC) therapy mean the relatively simple discrimination between small-cell and ‘non-small-cell’ carcinoma is insufficient to determine the best treatment for individual patients. Safety, efficacy and prescribing requirements mandate more specific subtyping of NSCLC for several new drugs: practice made difficult by the tumour heterogeneity combined with the paucity of tissue in most diagnostic samples. Immunohistochemical approaches have emerged as accurate predictors of probable tumour histotype. P63 and/or cytokeratins 5 and 6 and thyroid transcription factor 1 (TTF1) are among the best predictors, respectively, of squamous and adenocarcinoma histology. Molecular characteristics may predict response to both newer molecular targeted agents and traditional cytotoxic agents. Specific mutations in the epidermal growth factor receptor (EGFR) gene as predictors of response to EGFR tyrosine kinase inhibitors (erlotinib, gefitinib) is the first example of markers which predict response to targeted agents. Actual drug targets [e.g. thymidilate synthase (TS) – pemetrexed] or markers of the tumour’s ability to repair cytotoxic drug-induced damage [e.g. excision repair cross-complementation group 1 (ERCC1) – cisplatin] may well also complement NSCLC diagnosis. This extended diagnostic requirement from increasingly limited material provided by minimally invasive biopsy techniques poses major challenges for pathology.