Background Children with underlying malignancies and those on chemotherapy are at risk for having intestinal parasitic infections, which can lead to a severe course and death. This cross-sectional study was done to assess the copro-parasitological and copro-molecular prevalence of entero-parasites in children with malignancies and those on chemotherapy. Procedure Stool samples were collected from 137 Egyptian hospitalized cancerous children with different malignancies in the National Cancer Institute, and receiving chemotherapy. Faecal samples were examined microscopically. Genomic copro-DNA was extracted from fecal samples and amplified by 3 separate nPCR assays targeting Cryptosporidium , G. intestinalis and Entamoeba histolytica complex. Result The overall prevalence of enteroparasites was 6.6 % (9 cases). Only Giardia copro-DNA was encountered in 2 (1.4%) faecal samples of patients. Coproscopy detected parasites in 7 cases: Blastocystis spp. in 5 cases (3.6%), Hymenolepis nana in 1 case (0.7%) and Ascaris lumbericoides in 1 case (0.7%). Conclusion Low prevalence may be due to patient's use of prophylactic anti-parasitic and anti-fungal drugs, a standard protocol, basic hygienic practices and good nursing all of which are preventive against enteroparasites transmission. Among studied variables only diarrhoeic individuals who had a solid tumor, and soft/liquid stool with mucus and blood were predictors of intestinal parasitism.