Like other ciliates Paramecium has two kinds of nuclei: a large macronucelus, and one or more smaller micronuclei. The macronucleus is responsible for controlling cell cycles through RNA synthesis.

Although their entire function is not known, micronuclei are known to be essential for generating genetic variation during sexual reproduction. Paramecium can have up to 80 micronuclei.

A Paramecium has several food vacuoles that form at the end of the gullet and are used to hold ingested bacteria. Other vacuoles hold undigested materials until they can be expelled out of the anal pore at the posterior end of the cell. In the photo to the left, food vacuoles have been stained red.

Living in fresh water, Paramecium has a higher concentration of materials inside the cell than are present in the outside environment. Thus, water is constantly flowing into the cell through thr process of osmosis. Paramecium has two contractile vacuoles that eliminate water entering the cell by through osmosis and help maintain osmotic equilibrium.

Both contractile vacuoles are visible in the photo to the left. Paramecium must constantly be expelling water to prevent the cell from becoming bloated with water and potentially bursting.