Microfiltration was carried out in a newly-developed internal filter reactor system (stainless steel membrane filter, pore size=2 or 10 um) using yeast cells of Saccharomyces cerevisiae ATCC 24858, industrial S. cerevisiae, and recombinant yeast Rh 51. The filter per- formance was measured in terms of filtrate flux and retention coeffiient of cell, and was highly influenced by agitation speed and cell concentration. Both gel polarization model and solid flux model failed to predict the filtration behavior in the internal filter system. An empirical equation was obtained to correlate filtrate flux as a function of agitation speed and cell concentration. Retention coefficient with a filter of 2μm pore size was found more than 95%, and the filter was suitable for the yeast cell separation.