Idiopathic pulmonary fibrosis (IPF) is a progressive and devastating lung disease with a very poor prognosis. Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory airway disease and the third leading cause of death worldwide. Disease biomarkers are highly desired for IPF and COPD, especially in the early disease phase. Urine is an ideal biomarker source and has the potential to reflect small and early pathological changes. This chapter introduces the application of urine proteomics in the biomarker discovery of these two diseases. The findings will improve the understanding of the pathogenesis of IPF and COPD and accelerate urine biomarker discovery in respiratory diseases.