The aim of this study was to demonstrate the effect of medium chain saturated fatty acid (monolaurin) on experimentally infected Giardia lamblia and Entamoeba histolytica, and measurement of IFN-γ, TNFα, IL-4, IL-10, TGF-β levels of cytokines. To study the effect of monolaurin on the duodenal mucosa of the studied infected hamsters, a group of sixty golden Syrian hamsters were used, which were further divided into two subgroups: Subgroup I, in which hamsters were infected by oral administration of 10,000 G. lamblia cysts and Subgroup II, in which hamsters were infected by 10,000 E. histotytica cysts. Each subgroup was divided into (6) groups. Subgroup I included the group from (1 to 6), although subgroup II included from 7 to 12 groups. In G. lamblia infected subgroup I, best results were observed by the reduction in both vegetative and cystic forms, respectively shown in group (6) treated with combination of metronidazole and monolaurin post infection 94.68 and 96.55%, respectively. In the Subgroup II infected with E. histolytica, the high reduction in trophozoite and cystic forms in intestinal contents were in the group (12) which was treated with a combination of metronidazole and monolaurin post infection (90.12 and 92.56%, respectively). Cytokines levels IFN-γ, TNF-α, IL-4, IL-10 and TGF-β were measured in serum using sandwich enzyme-linked immunosorbent assay (ELISA). The best result was shown in the group (6) treated with a combination of metronidazole and mololaurin post infection 130,129, 35, 165 and 240 Pg/ml. Also histopathological examination gave the best healing in the groups (6) infected with G. lamblia than thos infected by E. histolytica.