A method for purifying a recombinant fusion protein that is expressed as recombinant protein body-like assemblies (RPBLAs) in host cells is disclosed in which an aqueous homogenate of transformed host cells that express a fusion protein as RPBLAs having a predetermined density is provided. Regions of different density are formed in the homogenate to provide a region that contains a relatively enhanced concentration of the RPBLAs and a region that contains a relatively depleted concentration of the RPBLAs. The RPBLAs-depleted region is separated from the region of relatively enhanced concentration of RPBLAs, thereby purifying said fusion protein. The region of relatively enhanced concentration of RPBLAs can thereafter be collected as desired.