Protozoans are single-celled eukaryotes. They are small organisms, ranging from a few microns in length up to about 1 mm. Therefore, the study of protozoans requires patience and skill as a microscopist. Specialized staining and optical techniques are often required to visualize their internal structures.

The basic body organization of protozoans consists of an external plasma membrane which encloses the cytoplasm and nucleus. There may be one or more nuclei, and in some taxa the nuclei are of two types: larger macronuclei and smaller micronuclei. Organelles present within the cytoplasm that are visible by light microscopy are few. Vacuoles containing food material in various states of digestion may be present, and mitochondria are occasionally large enough to be seen.

Three types of locomotory organelles may be present. One or more long flagella may be present. Cilia, shorter and more numerous than flagella are present in some taxa. Flagella and cilia aid in swimming. Pseudopodia, temporary extensions of the cytoplasm which elongate the plasma membrane, permit enable crawling.

Most protozoans pass through at least two distinct morphological forms during their life cycle. Much of the terminology for these forms is specific to particular taxa. Some terms are fairly general. Feeding stages are termed trophozoites, and these may reproduce asexually. Transmission stages enclosed within a membrane to resist conditions in the external environment are called cysts. Stages which are about to reproduce sexually and form gametes are called gametocytes.