In this study, we researched the effects of Bacillus subtilis and Bacillus amyloliquefaciens strains, which were produced, without any genetic modification, using the conditioning technique, on antibiotic induced diarrhea in rats. As part of the research, total aerobic mesophilic, total anaerobic mesophilic and total lactic acid bacteria analyses were performed on the stool samples taken from non-diarrheic, diarrheic and probiotic-administered diarrheic rats. The number of bacteria found in normal flora and antibiotic-inhibited flora was compared with the number of bacteria found in flora with Bacillus spores added, and it was determined that the latter inhibited the lactase-positive enteric bacteria and Staphylococcus and Micrococcus re-growth but did not prevent resettling of the anaerobic bacteria on the flora. In addition, when the total aerobic mesophilic bacteria counts were compared, it was found that a 2-log increase originated from the Bacillus species. The obtained biological activity and morphometry findings showed that the probiotic product prepared from the B. subtilis strain was highly effective in the microbial and antibiotic-associated diarrhea. It is therefore believed that significant medical and economic contributions will be provided through this study's complete analysis of the new probiotic product, which can be used in the treatment of various disorders, such as Clostridium difficile infection, irritable bowel syndrome and inflammatory bowel diseases.