Chronic obstructive pulmonary disease (COPD) is the most common chronic respiratory disease with a progressive course. The principal causes of COPD include cigarette smoking, environmental factors and genetic predisposition. Current knowledge about the development of inflammation, oxidative stress and protease-antiprotease imbalance is not sufficient to explain the origin and progression of the disease. In this study we found that cigarette smoke extract causes oxidative damage to cellular lipids and proteins in A549 alveolar epithelial cells, which could lead to the loss of important cell functions, eventually resulting in cell death. The accumulation of damaged proteins in cells leads to the activation of ER stress response in the form of increased levels of phosphorylated eIF2α and reduced de novo protein synthesis. It is likely that reduced protein synthesis contributes to the increase in the level of free amino acids in the cells, together with the degradation of proteins damaged by cigarette smoke inside the ubiquitin-proteasome system. ER stress response is usually associated with increased proteasomal activity; however, cigarette smoke causes a significant reduction in caspase-, trypsin- and chymotrypsin-proteasomal activities, making the proteasome inefficient in the process of removing damaged proteins. As a part of the cellular stress response, we observed an increase in the expression of chaperone proteins HSP32 and HSP27, which was not shown for HSP70. Likewise, we noticed the changes in MAPK signaling pathways: a significant increase in the level of activated p38, no activation of ERK and undetectable activation of JNK. Furthermore, the results showed that A549 cells do not produce MMP-9, but after a while treatment with the cigarette smoke extract increases the release of MMP-2 in the medium and decreases the release of TIMP-1, which probably contributes to the overall protease-antiprotease imbalance. In basal conditions polymorphonuclear leukocytes (PMN) of patients with COPD release significantly much more MMP-9 compared to healthy controls. Stimulation of PMN of healthy controls with cigarette smoke extract increases the release of MMP-9, while in patients with COPD no further increase over the high secretion rate was found, suggesting the chronic activation of PMN of patients with COPD and their possible role in the degradation of extracellular matrix in the lungs. Systemic protease-antiprotease imbalance in plasma of patients with COPD is manifested by increased concentration of MMP-9. ROC curve analysis showed a very good diagnostic accuracy for concentration of MMP-9, making it a good biomarker for distinguishing patients from healthy individuals. Testing the frequency of MMP9 gene polymorphisms (-1562 C/T and (CA)n dinucleotide repeat in the promoter region, and Q279R in exon 6) showed no significant difference between patients with COPD and healthy subjects, and no correlation of MMP-9 concentration with subjects’ genotypes. In sera of patients with COPD, with the observed systemic inflammation (increased total leukocytes, neutrophils and CRP), we found a decrease in activity of DPPIV, a protease that could be contributing to the development of inflammation. As showing a very good diagnostic accuracy, this enzyme could also be used as an effective biochemical marker of COPD.