The purpose of this work is to address the role of Auguste Comte’s biology in the development of the positive method of knowledge, exposed in the Cours de Philosophie Positive (1830-1842) through the classification of the sciences that organize the encyclopedia. The influence of this work on nineteenth-century thought is as undeniable as the rejection of its doctrine is today, especially from the use of the term “positivism” by the “empiricists or logical positivists” of the well-known Vienna Circle. However, paradoxically, the return of the naturalism at the end of twentieth century (Kitcher, 1992) and its great diffusion until our days, has promoted a re-reading of Comte since the study of Comte helps to clarify the implicit positivist assumptions in some of the so-called naturalist positions. Our aim is, therefore, to contribute to the understanding of Comtean positivism aiming to show that this analysis has relevance for current philosophy of science. In this sense, biology becomes especially pertinent. Within the encyclopedia, biology occupies the penultimate place, a scientific disadvantaged place according to Comte, but an epistemologically ́strategic ́ position for most of his current commentators. This science is the link between the studies related to the inert world and those that refer to the living world. Within it, we will pay special attention to the last section, i.e., cerebral physiology, because in it the subordination of analytical methods by synthetic methods for the study of knowledge takes place. This subordination supposes, according to Comte, the end of the “fatal antagonism” between the conceptions referring to man and those referring to the “external world”. Therefore, the relevance of this science is linked within the encyclopedia, to the possibility of establishing the general system of knowledge for which the Cours was created; and within current philosophy, to the possibility of shedding light on the conceptual foundation of current naturalistic positions.