This study was conducted to identify the latest pharmacological agents available for the chemotherapy of pathogenic protozoa affecting the human intestine, specifically targeting Entamoeba histolytica and Cryptosporidium parvum. For the treatment of amoebiasis caused by E. histolytica, modern drugs include diloxanide furoate, iodoquinol (diiodohydroxyquin), and paromomycin, which are primarily used to eliminate intestinal cysts in the lumen. Metronidazole, tinidazole, and nitazoxanide are employed to eradicate tissue trophozoites of E. histolytica. For amebic liver abscesses or extraintestinal infections, the recommended drugs are paromomycin, metronidazole, emetine, and chloroquine. In pregnant women with amoebiasis, treatment should involve a tissue amebicide such as metronidazole, followed by a luminal agent like paromomycin after the first trimester, or second-line agents such as diloxanide furoate or iodoquinol.