The chemist Louis Pasteur (1822-1895) devoted himself to studies as crystallography, fermentation, spontaneous generation, silkworms’ disease, rabies, avian cholera, anthrax, among others. In many of these works, we see the microorganism as the protagonist. However, the design of the action and the nature of these microorganisms are different in the cases covered in this study. At the beginning of his work on fermentation, Pasteur refers to this process as a "mysterious phenomenon" and through his research he relates the microorganism to the fermentation. Pasteur related this phenomenon to medical applications, whereas fermentation and disease were similar procedures. In the early nineteenth century evidence emerged that diseases could be caused by microscopic parasites. Before that, the microorganisms were observed in sick organisms but they were initially considered as a consequence of the disease rather than its cause, as happened in the studies of Pasteur on the silkworm disease, the first disease studied by him, in 1865. Initial work of Pasteur on microbiology was related to the parasitological nature of the pebrine, in which he noted the existence of microscopic corpuscles in the body of sick caterpillars. During research on the silkworm, the presence of the microorganism in sick caterpillars was not related to the disease. Later, Pasteur devoted himself to studies about rabies. In this case the microorganism appears, within the concepts of Pasteur, as the causative agent of the disease. This research was of great importance for the development of the germ theory of disease in the latter half of the nineteenth century. The objective of this paper is to discuss these different conceptions about the microorganisms that are present in the work of Pasteur, and analyze the factors that led to several changes in conceptions about the nature of microorganisms related diseases, their prophylaxis and to the development of vaccines. This research is part of larger projects developed by the CESIMA, with support from CAPES (PhD scholarship).