Inclusion bodies are a source of large quantities of protein with high purity over-expressed in Escherichia coli. Efficient solubilization is the initial step in recovering the protein. We visualized solubilization using high-resolution light and transmission electron microscopy over time and the most common solubilization agents, urea and guanidine hydrochloride, as well as sodium hydroxide. Upon solubilization, the inclusion bodies were penetrated by the solubilization agent, shrinking the densely packed cores as the protein diffused out. Despite the complex process, solubilization could be described by a homogeneous layer model with a high order of reaction. The solubilization of protein aggregates, such as inclusion bodies, does not follow the rules of ordinary solubilization processes, but is controlled by pore diffusion. Consequently, power input and mixing frequency is not relevant to the process. (C) 2013 Elsevier Ltd. All rights reserved,