The guttural pouches are outpouchings of the eustachian tube and are peculiar to the Perissodactyla (horse, tapir, rhinoceros). They are the site of several pathological conditions including mycosis, empyema, and tympany in modern horses.
One can say that the modern horse has been predisposed to disease of the guttural pouches by the evolution of high-crowned hypsodont teeth and the narrow deep skull configuration needed to accommodate those teeth. That requires some explanation.
During the Miocene period, about 20 million years ago, the evolving horses began to change from browsers--eating leaves, bushes, and twigs like modern deer--to grazers as we know them today. That change occurred because the environment in which the horses found themselves changed, gradually but markedly, from forest and swamp to savannah and open grasslands.
With the change (and remember we are talking thousands and millions of years), the short, low-crowned brachydont teeth of the browser were replaced by long, high-crowned teeth with greater abrasion resistance. That was necessary, of course, because grasses contain silica--a very abrasive material--and the longer tooth was needed to last the lifetime of the horse.
In order to accommodate those longer teeth, the skull of the horse became deeper and narrower. The pharynx became deeper and narrower as well, as a result of which swallowing was compromised. Skoda, an Austrian anatomist, showed in 1911 that the narrow pharynx of the horse was not attached firmly to bone as in other species and moved considerably during swallowing. This movement was necessitated by the long, narrow pharynx so that a bolus of food could pass from mouth to esophagus without entering the larynx.
Skoda further showed that movement could be accomplished because the wall of the pharynx was attached to the flexible walls of the guttural pouches. He proposed (and his theory has not been refuted) that the guttural pouches developed primarily as a necessary aid to swallowing. Abnormal swallowing does occur with tympany, empyema or inflammatory disease of the guttural pouches, which supports, but does not prove, Skoda's hypothesis.
That might not be the only reason for the presence of guttural pouches, but it is a good reason, and the only one for which we have both experimental and theoretical evidence.
Reprinted from Equine Disease Quarterly.