This article aims to describe and analyze the implementation of hygienic and sanitary measures in the Ejercito del Sur, which occupied La Araucanía in the second half of the 19th century. This historical process of territorial and political control preceded and developed in the company of other military campaigns such as the Guerra del Pacifico, and in general, was one of the expressions of the medicalization of Chilean society framed within what we could define as a hygienist paradigm in service of the State. Dominating territories and governing populations was the main purpose of the State. That’s why hygienism, in its moral, prophylactic, environmental, and sanitary aspects, proved to be of great utility. Through the analysis of these latter expressions of hygienism in the Ejército we seek to understand the development of military medicine, for which we have consulted a series of documents from military reports and medical journals from the period.