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This article presents results of the influence of three probiotic feed additive of various microbiological composition: Bacillus subtilis (VKPM B‐2335); B. subtilis (OZ‐2 VKPM‐11966) + Bacillus amyloliquefaciens (OZ‐3 VKPM‐11967); Lactobacillus acidophilus (VKPM B‐3235) on the growth and histology of the organs of the gastrointestinal tract of juvenile Oncorhynchus mykiss by morphometric parameters. These probiotic bacteria are the most commonly used in aquaculture. The effect of the probiotic feed additive led to the increase in fish growth and influenced different sections of the gastrointestinal tract. The biggest change was found in the mid intestine and the reliable difference compared with the control diet was obtained at the following parameters: lamina propria width, intraepithelial lymphocytes number of prismatic epithelium and goblet cells area. The changes in the pyloric appendages were less obvious but reported as playing an important functional role in digestion. The liver preserved normal functional structure in all series of the experiment except for the group with L. acidophilus, where hepatocyte small‐drop vacuolization was observed. That might be connected with the change of the digest activity resulting from a decrease in secretory activity of the intestinal exocrinocytes. The use of all probiotic feed additives led to a similar change in morphometric parameters in all groups, which suggests a decrease in the immune response.