Objectives: To detect enteric protozoal species in stool samples of children affected by malignancies who are receiving chemotherapy compared to healthy children and to investigate differences in the infection rates among different cancer types. Materials and Methods: This study included 100 children diagnosed with malignancy under chemotherapy attended Ibn-Al-Atheer Teaching Hospital during the period from December 2013 to June 2014. The study also included 50 apparently healthy children as a control group who were age and gender matched to the cancer patients. Children were already diagnosed as having malignant disease by consultant oncologists and receiving chemotherapy. A Questionnaire Form was completed for each child. Stool samples were taken from patients and controls to detect protozoal infections. The stool was tested by direct wet mount preparation, iodine staining, and concentration methods, hot modified Ziehl-Neelson staining method was also used to detect the acid-fast oocysts of Cryptosporidium. Results: Enteric protozoal infection was detected in 60 (60%) of patients compared to 5(10%) of controls (p<0.05). Four protozoal species were observed among patients included G. lamblia representing (24%), C. parvum (19%), E. histolytica/E. dispar (5%), and B. species (5%). Whereas in the control group, included G. lamblia (6%), C. parvum (2%), and B. species (2%). The highest infection rate was found among children with lymphoma (77.27%), followed by (62.26%) and (40%) among patients with leukemia and solid tumors, respectively (p>0.05). Conclusions: The incidence of enteric protozoal infections is higher among cancer children than healthy group and dominates by Giardia lamblia and Cryptosporidium parvum, but other species including E. histolytica/ E. dispar and B. hominis are also found. Patients with lymphohematopoietic malignancies show the highest infection rates.