The amoeba and ciliates are protozoan parasites that have been causing illness in humans since antiquity. The most relevant foodborne parasites of these groups are Entamoeba histolytica and Balantidium coli. Entamoeba dispar has been identified mostly in asymptomatic patients however, reports demonstrating invasive amebiasis caused by E. dispar may indicate various levels of pathogenicity. In recent years, studies on the pathogenesis and immune responses to amoebiasis are providing insights on how to control this parasitosis that affects more than 50 million people annually.This chapter will address the various aspects of these parasites, from the biology, life cycle, clinical presentation, and treatment.