The paper compares Auguste Comte’s and Franz Brentano’s views on the following issues: the classification of phenomena and of the sciences, the criterion of the fundamental division of phenomena and the change of method implied by it. It is argued that the hierarchy of phenomena in Comte is based on three principles: the principles of dependency, of continuity, and of emergence. Within this hierarchy lies the fundamental separation of phenomena between the inorganic and the organic, i. e., between milieu and organism. On the contrary, Brentano recognizes the dependence of the psychological on the physiological and the emergence of the former on the basis of the latter, but there is no continuity between the two realms for him, because the psychological phenomena are absolutely heterogeneous from the physiological and from the physical phenomena in general. Brentano’s basic division of the hierarchy of phenomena is therefore not between chemical (inorganic) and biological (organic) phenomena, but between physiological phenomena and mental phenomena. In contrast to Comte, for whom each new order of phenomena is built upon and really contains the order of phenomena preceding it in his scale, Brentano’s mental phenomena contain all other phenomena not really, but only intentionally. Whereas, for Comte, organization constitutes the criterion that separates the inorganic from the organic world, for Brentano the mental world is separated from the physical world not on the basis of organization but on the basis of intentionality and is closely connected with the separation res extensa-res cogitans in Descartes. This is further closely connected with the fact that in both authors the mentioned separations involve a change of the scientific method: in Comte’s case, one passes from the analytical to the synthetic method, but in Brentano’s case from observation and experiment as the method of natural science to inner perception and study of psychic phenomena in fresh memory as the method of mental science.