The effects of ciliate protozoa on the ruminal ecosystem, digestion in different parts of the gut, the nature of nutrients available for absorption and their effects upon the nutrition and productivity of their host are reviewed. Compared with fauna-free ruminants, the presence of ciliate protozoa results in a more stable ruminal fermentation, higher levels of ammonia, reduced numbers of bacteria, as well as changes in dry matter (%), liquid volume and turnover rate of ruminal contents. Associated with these differences in the rumen are higher ruminal and total tract digestion of organic matter and fiber in faunated animals. A reduction in net microbial synthesis and an increase in dietary protein degradation in the rumen results in the flow of protein to the small intestine being lower in faunated ruminants. The major nutritional effect of the ciliate protozoa is to change the ratio of protein to energy in the nutrients absorbed, with faunated animals having lower protein and higher energy availabilities compared with ciliate-free ruminants. Of the nutrients available for absorption, the ciliates have no consistent effect on the proportions of volatile fatty acids or amino acids. However, there is evidence that hydrogenation of lipids is increased, as is the supply of choline, and that the bioavailability of copper is reduced by the presence of ciliates. Defaunation of young growing ruminants that are fed high energy diets, containing low levels of ruminal nondegradable protein, results in increased growth rate and feed efficiency. It is unlikely, with the possible exception of wool growth, that there are other situations in which defaunation will be beneficial; and it is more likely to be detrimental to animal productivity. It remains to be determined whether manipulation of the types of ciliate protozoa in the rumen could improve animal performance. Information for this review was largely derived from comparisons of faunated and fauna-free animals. However, it is indicated that there are large differences in protozoa numbers and types between naturally faunated individuals in the same flock or herd, and that the effects of such variations on their host's nutrition are unknown.