Ciliates have only one opening on their single-cell bodies where food can enter. It is called a cytostome, meaning "cellular mouth". Food are usually directed into the cytostome by cilia lining an elongated furrow in the cell surface called the oral groove. Ciliates eat constantly and will consume enormous amounts of food in relation to their own body weight.

Once inside the oral groove, the food is ingested by phagocytosis. Enclosed in a vacuole, the food is carried through the body along a specific path first anteriorly and then posteriorly. At first, acids and digestive enzymes are secreted into the vacuole to partially digest some of the food. Then, after a few minutes to hours, the acids are neutralized by alkaline secretions for further digested by alkaline active enzymes. This process is similar to a human digestive system, where acid is present in the stomach and alkaline is present in the intestine.

After digestion is complete, the food vacuole contacts the cell membrane at the cytoproct ("cellular anus"), and its undigested contents are expelled from the cell into the surrounding medium.

Ciliates must hunt their food in a variety of environments. Many species, such as the well-known ciliate Paramecium, eat bacteria. A single Paramecium may consume up to 5000 bacteria each day. Suctorians (at right) are ciliates that are anchored to the substrate and use their extended tentacles to capture passing prey. Upon contact, the suctorians inject the prey with poison and immoblize them, then suck the cytoplasm from the prey organism