Blastocystis spp., a protozoan parasite are common around the world. Metronidazole has been commonly used in treatment of Blastocystosis. Recently it has been reported that metronidazole treatment failed in some patients. Therefore, this finding would be related to resistance to metronidazole. This study aims to investigate viability of Blastocystis spp. following treatment with ornidazole, ciprofloxacin, and trimetroprim-sulfamethoxazole (TMP-SMX) and metronidazole. Viability of the parasite was measured using MTT assay (Cell Proliferation Kit MTT, Roche, USA). Stool samples from three cases where Blastocystis spp. (A,B,C) had been detected in native-lugol examinations were incubated in culture medium. Then the parasites were transferred into a fresh medium containing antibiotics and antifungals. Microbiological culture mediums were used checking for bacterial contamination. On a 96- well microplate, serial dilutions of drugs were prepared and parasites were added into wells. The resistance behaviour of every strains was differentiated. While ciprofloxacin was the most powerful anti-parasitic drug on the viability of strain A,TMP-SMX and ornidazole were highly effective on strain C. Viability of strain B was not to affected by concentration of the drugs. We concluded that standardized sensitivity test for anti-parasitic drugs was needed for effective treatment of Blastocystosis.