Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) can be used to analyse peptides and proteins in clinical samples. A prospective study was undertaken on patients undergoing curative resection for non-small cell lung cancer (NSCLC): we used SELDI-TOF-MS to compare the proteomic profiles of serum from these patients both before surgical resection and after resection (disease-free) to identify potential biomarkers. Student t-tests were used, and a P-value of <0.01 was considered significant. Twenty-five patients with NSCLC [76% male, mean age 69 (range 53-81) years] were analysed. There were 13 squamous cell carcinomas, 10 adenocarcinomas and 2 large cell carcinomas with a stage distribution of four stage IA, 11 stage IB, five stage IIB, three stage IIIA, one stage IIIB and one stage IV. SELDI spectra generated with immobilised metal affinity chromatography arrays produced 170 peaks. Of these, 35 showed significant differences in their intensities between the preoperative and post-resection states (P<0.01). Postoperative samples in the disease-free state may represent good controls to identify biomarkers in NSCLC, avoiding the difficulties associated with cross-sectional studies. These pilot data need to be validated with larger numbers of patients.