In developing countries, the prevalence of intestinal parasitic infection is still significant, particularly due to geographical and socioeconomic variables. The objective of this study was to map the distribution pattern of intestinal parasitic infection in a cohort of the Egyptian population, as well as to assess associated risk factors. A cross-sectional hospital-based study was conducted on 386 patients. A single fecal specimen was collected from the study individual and examined microscopically for the detection of parasitic infection. DNA was extracted from all samples and utilized to amplifyEntamoeba histolyticacomplex species, Cryptosporidiumspecies,Giardia intestinalisassemblages, andBlastocystisspecies using PCRs. Typing ofCryptosporidium speciesandGiardia intestinalisassemblages was performed using restriction enzymesRasIandHaeIIIrespectively. WhileBlastocystisspp. subtypes (ST) were identified through sequencing of PCR products and phylogenetic analysis. 59.6% (230/386) of the study patients were infected with one or more intestinal parasites, 87.4%; 201/230 of patients had mono-parasitic infections, and 12.6%; 29/230 had multiple-parasitic infections (P< 0.0001). The predominant protozoa wereBlastocystis, followed byEntamoeba histolyticacomplex, andGiardia intestinalisboth as mono-parasites and as part of multiple parasites. Molecular assays showed thatBlastocystisST3,Entamoeba dispar,Giardia intestinalisassemblage B, andCryptosporidium hominiswere the most prevalent species. Intestinal parasitic infection was significantly associated with age, gender, residence, and water source. Multi-parasitism showed that residency in a rural area was a risk factor (OR 4.49; 95% CI 1.51–13.37;P= 0.007). Egyptians residing in rural areas have a high prevalence of intestinal multi-parasitism. Therefore, to lessen the prevalence and effects of these infections in this group, effective and sustainable control methods, providing health education focusing on good personal hygiene habits, and providing a safe drinking water supply should be implemented.