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Vertical changes of aerosol concentration and size in the free troposphere over the Asian desert areas were firstly observed using a balloon-borne optical particle counter at DunHuang, China (40°00′N, 94°30′E) (17 August and 17 October 2001, and 11 January 2002). In the free troposphere highly concentrated aerosol layers were frequently observed, suggesting the importance of regional scale particle transportation over the Asian continent. Concentration of particles with a diameter larger than 0.15 μm was about 5–10 particles cm-3 in the free troposphere. Particle number-size distribution in the free troposphere shows important contribution of super micron particles. Regional scale transportation, in addition to diffusion of soil particles from the lower atmosphere to the free troposphere through local and small scale air motions, is suggested by backward trajectory analysis of air masses containing super micron particles. The importance of horizontal transport of coarse size particles in the free troposphere was strongly suggested. Thickness of the boundary mixing layer, from distributions of particle concentration, was about 4 km in summer (17 August 2001) and apparently higher than the height of layers in fall (17 October 2001) and in winter (11 January 2002), which suggest an active mixing of particles near the boundary in summer. In winter measurement (11 January 2002), strong inversion was found in the vertical profile of temperature, suggesting cold ground surface and vertically stable atmosphere near the ground.