Parasitic infections in children with liver diseases could be a serious health problem. This study documented a true prevalence of intestinal parasitosis in children with pediatric liver diseases and estimate risk factors for parasitic infection. Faecal samples were collected from 95 children suffering liver diseases. Samples were examined microscopically for parasitic stages and coproscopy of acid fast (AF) stained fecal smear for Cryptosporidium oocysts, by ELISA for E. histolytica and Giardia and by PCR genotyping for E. histolytica and Cryptosporidium spp. copro-DNA. G. intestinalis was the prevailing protozoa (14.7%) followed by Hymenolepis nana (8.4%) and C. hominis (4.2%). The pathogenic E. histolytica was not detected by genetic differentiation or ELISA. Only age group (P value .004) was a risk factor for intestinal parasitosis among these children. Giardiasis, hymenolepiasis nana and cryptosporidiosis are the most prevailing parasites in children with liver disease that physicians must consider. Accurate diagnosis using molecular technique is a must with E.histolytica and helpful with Cryptosporidium genotyping for epidemiological purposes.