Cell adsorption and selective desorption for separation of microbial cells were conducted by using chitosanimmobilized silica (CIS). When chitosan was immobilized onto silica surfaces with glutaraldehyde, bacterial cells adsorbed well and retained viability. Testing of the adsorption and desorption ability of CIS using various microbes such as Escherichia coli, Aeromonas hydrophila, Pseudomonas aeruginosa, Bacillus subtilis, Micrococcus luteus, Staphylococcus aureus, Staphylococcus epidermidis, Lactobacillus casei, Streptococcus mutans, Streptococcus sobrinus, Streptococcus salivarius, Saccharomyces cerevisiae, Saccharomyces ludwigii, and Schizosaccharomyces pombe revealed that most microbes could be adsorbed and selectively desorbed under different conditions. In particular, recovery was improved when L-cysteine was added. A mixture of two bacterial strains adsorbed onto CIS could also be successfully separated by use of specific solutions for each strain. Most of the desorbed cells were alive. Thus, quantitative and selective fractionation of cells is readily achievable by employing chitosan, a known antibacterial material.Infection and contagion are becoming increasing problems in our communities, for example, with nosocomial infections caused by antibiotic bacterial strains like methicillin-resistant Staphylococcus aureus, mass food poisoning caused by contaminating pathogenic bacteria like enteropathogenic Escherichia coli O157 in water or foods, and infections caused by the microscopic parasites Giardia and Cryptosporidium, which are found in water. Traditionally, these microorganisms can be found by culture-based methods, such as single-colony isolation and antibody utilization using an enzyme-linked immunosorbent assay (4,5,21). Recently, PCR has been commonly applied (9,11,12). Furthermore, various methods, such as differential staining, serological methods, flow cytometry, phage typing, protein analysis, and comparison of DNA nucleotide sequences, have been utilized. These methods enable us to detect microbes in small samples with high sensitivity (3).At the industrial level, these approaches are not suitable due to limited time and the significant effort, cost, and scale involved. The culture-based method is restricted to viable target bacteria and is time-consuming. Therefore, it is of great interest to develop novel fast and inexpensive detection, separation, and isolation methods (1,7,10).The purpose of the present study was to assess a new separation and concentration system for bacterial cells that is easy to apply and allows rapid processing by using chitosan as a functional ligand. Our final purpose in this study was to fractionate microbial cells with chitosan.