The recovery of therapeutic recombinant proteins from E. coli typically involves the harvesting of intact cells from bioreactors and subsequent recovery of inclusion bodies following cell disruption. Currently, the efficiency of E. coli disruption and recombinant protein granule release achieved following homogenization is measured using phase contrast microscopy and manual counting. This technique is low-throughput, subject to operator error, and poses significant ergonomic stress.  Flow cytometry and nuclear staining enables high-throughput, sensitive and reproducible quantitation of intact E. coli, disrupted E. coli and released inclusion bodies within a sample.  This technique allows investigators to establish the true manufacturing process baseline and enables them to explore different process parameters that might improve homogenization efficiency and, ultimately, recombinant protein yield.