Background The aim of this study was to prospectively study the changes in neutrophil elastase (NE), fibroblast growth factor 9 (Fgf9), matrix metalloproteinase-9 (MMP-9), tissue inhibitor of metalloproteinase 1 (TIMP-1) in sputum induced during the early period after lung volume reduction surgery (LVRS). Methods From April to October 2005, ten consecutive patients with chronic obstructive pulmonary disease (COPD) underwent LVRS. Ten non-small cell lung cancer patients (stage II-IIIa) received lobectomy as a control group. The induced sputum was collected from both groups at six different times (two weeks before operation and postoperatively at 1, 2, 4, 6 and 10 days). The level of NE, Fgf9, MMP-9 and TIMP-1 were measured using enzyme-linked immunosorbent assay. Results The pulmonary function (FEV1%) and arterial blood gases (PaO2 and PaCO2) were significantly different between the groups. There were no significant differences in age, ejection fraction (EF), and operation duration, but hemoglobin in the LVRS group was statistically higher than in the controls. At certain times, there were significant differences in NE, MMP-9, TIMP-1 and MMP-9/TIMP-1 (P <0.05) but not in Fgf9 between the two groups. The levels of NE and TIMP-1 were maximal at 2 days postoperatively and that of MMP-9 and MMP-9/TIMP-1 at 4 days postoperatively in the LVRS group. In the control group, maximal levels of NE and TIMP-1 occurred at 2 days postoperatively and that of MMP-9 and MMP-9/TIMP-1 at 1 day postoperatively. Ten days after surgery, all values of the control group were not significantly different from the baseline. In the LVRS group, the levels were significantly different from the pre-operative values (P <0.05) apart from TIMP-1. Conclusion The levels of NE, MMP-9, TIMP-1 and MMP-9/TIMP-1 of the LVRS group were different from those of the control group. The time course of these changes may be related to LVRS and the underlying process of COPD.