Respiratory diseases threat to human life safety seriously, at present there is no good treatment for a number of diseases such as acute lung injury, pulmonary hypertension. Cell replacement and gene therapy is the development trend of the future. Bone marrow mesenchymal stem cells as a widely used stem cells have unlimited potential applications in acute lung injury, pulmonary hypertension and asthma therapy. In this paper, a brief overview on the latest progress of stem cell therapy for these diseases.