'balantidium' originates from New Latin, ultimately from Greek 'balantidion', a diminutive of 'balantion', where 'balantion' referred to a small bag or pouch (used for shape reference).

'balantidium' was adopted in New Latin for zoological classification in the 19th century from Greek 'balantidion'; it became the modern scientific genus name 'Balantidium' used in microbiology and parasitology.

Initially the Greek root referred to a small bag or pouch (shape-related); over time the term was applied in taxonomy to name this genus of pouch- or ovoid-shaped ciliates and now denotes the protozoan genus (and related disease when specifying species).