In this research, Cetyl Trimethyl Ammonium Bromide (CTAB), as an antimicrobial agent, applied on polyester, polypropylene and viscose non-woven fabrics. Also, CTAB coapplied with a fluorochemical based water repellent agent namely FC1112. The antimicrobial, water and blood repellency of the treated samples were investigated. To reveal the antimicrobial properties of the treated samples, the zone of inhibition and reduction of bacteria were measured with S. aureus, E. coli and P. aeroginosa. The results showed a good antimicrobial property on different concentration of CTAB solutions (1%, 2%, 4% and 8%). Application of CTAB with concentration of (0.5%, 1% and 2%) on polyester, polypropylene and viscose nonwoven fabrics indicated a reasonable antimicrobial effect. Co-application of CTAB with fluorochemical on different samples also showed a good antimicrobial, water and blood repellency properties.