Urine is a promising resource for studying biomarkers of acute and chronic inflammatory diseases of the respiratory system. In this chapter, we investigated the dynamic changes in the urinary proteome during acute and chronic pulmonary inflammation, such as ventilator-induced lung injury (VILI) rats, OVA-induced asthma mice, and CS-induced COPD rats. In VILI rats, 13 proteins were identified as candidate biomarkers for VILI through PRM validation. Among these PRM-validated proteins, AMPN, MEP1B, LYSC1, DPP4, and CYC have been previously reported as lung-associated disease biomarkers. Newly discovered in this chapter were SLC31, MEP1A, S15A2, NHRF1, XPP2, GGT1, HEXA, and ATPB. In OVA-induced asthma mice, after two episodes of OVA sensitization (on days 2 and 8), six differential proteins (CRAMP, ECP, HP, F2, AGP1, and CFB) were reported to be closely associated with asthma. These proteins may hold the potential for early screening of asthma. After being challenged with 1% OVA by inhalation (on days 15 and 18), seven additional differential proteins (VDBP, HP, CTSE, PIGR, AAT, TRFE, and HPX) were also reported to be closely associated with asthma, indicating their potential as biomarkers for diagnosing asthma attacks. In CS-induced COPD rats, seven proteins that changed at weeks 2 and 4—when there were no changes in pulmonary function or pathological morphology—were verified as potential biomarkers for early screening of CS-induced COPD through proteomic analysis. Another six proteins that changed at week 8, when obvious airflow obstruction was detected, were verified as potential biomarkers for prognostic assessment of CS-induced COPD. Our results reveal that the urinary proteome can sensitively reflect pathophysiological changes in the development of VILI, asthma, and COPD and may advance our understanding of the pathogenesis of these diseases. Importantly, we identified candidate urinary biomarkers that could be utilized for early screening, diagnosis, and/or prognosis of VILI, asthma, and COPD.