Microsporidian pathogens are obligatory intracellular eukaryotic parasites which can be found worldwide. They have been represented in 144 genera and more than 1200 species that may cause infections in both vertebrate and invertebrate hosts. Enterocytozoon bieneusi and Encephalitozoon intestinalis are the most common species among 14 species of microsporidia identified as human pathogens and they cause infections in the gastrointestinal tract. These species may also cause chronic diarrhea particularly in immunocompromised patients, as well as disseminated infections with severe clinical conditions which can be life-threatening. Since the spores of microsporidia are quite small-sized structures, they frequently may be overlooked in routine stool examinations. Therefore, molecular methods and transmission electron microscopy, if possible, are used as the gold standard methods in laboratory diagnosis. In laboratories in which those methods could not be applied, immunofluorescence assay using monoclonal antibodies (IFA-MAbs) may be advantageous compared to conventional methods. The aim of this study was to investigate the presence of Eintestinalis and Ebieneusi in bone marrow transplant (BMT) patients by using IFA-MAbs method. A total of 200 BMT patients (134 male, 66 female; mean age: 43.2 15.01 years), of them 147 with diarrhea and 80 healthy subjects (43 male, 37 female; mean age: 31.9 11.76 years) as control group were included in the study. All of the stool samples were examined by a commercial IFA-MAbs (Bordier Affinity Products, Switzerland) method as well as conventional (native-lugol and modified acid-fast staining) methods. Of the patients 25.5% (51/200) were positive for Eintestinalis, 4% (8/200) for E.bieneusi and 9.5% (19/200) for both of them, giving a total positivity rate of 39% (78/200). Those rates were 5% (4/80), 2.5% (2/80), 3.8% (3/80) and 11.3% (9/80), respectively for control group. The difference between the patient and control groups in terms of positivity was found statistically significant (39% vs 11.3%, p< 0.05). Among 78 positive BMT patients, 67(85.9%) were suffering from diarrhea. The correlation between the presence of diarrhea and the presence of microsporidia was statistically significant (p< 0.05). It was concluded that, BMT patients particularly those with gastrointestinal complaints, have to be evaluated for microsporidian pathogens regularly to improve quality of life and to decrease the problems during the treatment period.