Exhaled volatile organic compounds (VOCs), mainly aliphatic and aromatic hydrocarbons, have been proposed as a diagnostic test for early lung cancer detection, but the effect of lung cancer surgical re-moval on exhaled VOCs pattern has never been specifically addressed. The aim of this study was to compare VOC levels measured in non small cell lung cancer (NSCLC) patients before surgery (T0), one month (T1) and 3 years (T2) after surgical removal of tumour. In order to better understand the pathophysiological meaning of exhaled aromatic hydrocarbons, the same exhaled biomarkers were also assessed in cancerous and macroscopically unaffected lung tissue samples collected during surgical operation. Exhaled breath was collected in a specially designed Teflon bulb trapping the last 150 ml of a single slow vital capacity. After solid phase micro-extraction, VOCs were analysed in gas chromatography-mass spectrometry. VOC levels were unaffected by surgical removal, except for isoprene, whose concentration was significantly reduced. Three years after surgical operation, some VOCs significantly changed from baseline: in particular, we noted a decrease in isoprene and benzene concentrations, whereas the levels of pentane, toluene and ethylbenzene were increased in comparison with baseline values. Finally, lung tissue analysis showed that all aromatic hydrocarbons, except xylenes, were significantly higher in cancerous than in unaffected tissue. This study showed that surgical operation can influence the concentration of some exhaled VOCs opening a new scenario in the use of exhaled VOCs in lung cancer patients, not only for diagnostic but also for follow up purposes.