Helicobacter pylori (H. pylori) and intestinal parasites are known for their high prevalence in children. Both of them infect the gastrointestinal tract with overlapping clinical pictures. This study was conducted to determine H. pylori prevalence and its association with intestinal parasites in children, moreover to estimate risk and predictive factors for their detection in stool samples. Single fecal samples were collected from 226 Egyptian pediatric patients (125 diarrheic and 101 non-diarrheic) attending gastroenterology outpatients' clinics, from February 2016 to June 2017. All stool specimens were microscopically examined to search for ova and parasites. Copro-DNAs detection of H. pylori and Cryptosporidium were performed using nested-PCR assays. H. pylori was detected molecularly in 36.8% of the total study population, with a higher prevalence in diarrheic than in nondiarrheic children. Intestinal parasites were detected in 27.4% of the total study populations, of these, 43.9% had co-existence with H. pylori colonized patients and was significantly associated with Cryptosporidium spp. and G. intestinalis. Estimated risk of the presence of H. pylori was in January. Our data provide a better understanding of the epidemiology of H. pylori infection when associated with intestinal parasites. H. pylori co-existence with G. intestinals and Cryptosporidium may suggest the association of H. pylori infection with markers of fecal exposure. Whether H. pylori provides favorable conditions for intestinal parasitosis or vice versa, still further investigations are needed with an emphasis upon determining correlation with gut microbiomes.