The effect of Blastocystis hominis (B. hominis) in both immunocompetent and immunocompromised subjects has been the subject of debate in recent years, mostly in response to its unknown pathogenicity and frequency of occurrence. We performed a non-randomised, open labelled, single institute study in our hospital in order to investigate the clinical significance and frequency of B. hominis in patients suffering from hematological malignancy (HM) who displayed symptoms of gastrointestinal diseases during the period of chemotherapy-induced neutropenia. The presence and potential role of other intestinal inclusive of parasites were also studied. At least 3 stool samples from each of 206 HM patients with gastrointestinal complaints (the HM group) were studied. These were compared with stool samples from a control group of 200 patients without HM who were also suffering from gastrointestinal complaints. Samples were studied with saline-lugol, formalin-ether, and trichome staining methods. Groups were comparable in terms of gender, age and type of gastrointestinal complaints. In the HM group, the most common parasite was B. hominis. In this group, 23 patients (13%) had B. hominis, while in the control group only 2 patients (1%) had B. hominis. This difference was statistically significant (P < 0.05). Symptoms were non-specific for B. hominis or other parasites in the HM group. The predominant symptoms in both groups were abdominal pain (87-89.5%), diarrhea (70-89.5%), and flatulence (74-68.4%). Although all patients with HM were symptom-free at the end of treatment with oral metranidazol (1,500 mg per day for 10 days) 2 patients with HM had positive stool samples containing an insignificant number of parasites (< 5 cells per field).