This large and diverse group includes some of the most complex protozoans known such as Paramecium, Stentor, Spirostomum and Vorticella. Locomotion is always by cilia, and all forms are multinucleate, having at least one macronucleus (responsible for metabolic and developmental functions of the cell) and one or more micronuclei that are involved in sexual reproduction). Most are holozoic but a few forms are parasitic and cause damage to their hosts, including humans. Several parasitic species can cause serious problems for aquarium fish and fish in farm enclosures.

In addition to a number of complex organelles, many ciliates have a sculptured, rigid outer covering called a pellicle. Embedded in the pellicle are the cilia plus a number of thread-like structures called trichocysts. Upon mechanical or chemical stimulation, these trichocysts can be discharged to produce long, sticky protein threads that remain attached to the organism. Although the function of these structures is probably defensive, it has been hard to demonstrate this.