Nisin is a bacteriocin marketed as Nisaplin. The aim of our work was to test its in vivo effect in a rabbit model; its effect on phagocytic activity (PA) and morphometry has not so far been studied. Post-weaning rabbits (48), 5 weeks old (both sexes, Hycole breed), were divided into the experimental (E) and the control groups (C), 24 animals in each. They were fed a commercial diet with access to water ad libitum. Rabbits in E had nisin additionally administered to their drinking water (500 IU-20 μg per animal/day) for 28 days. The experiment lasted 42 days. On day 28, significant decrease in coagulase-positive (CoPS) staphylococci and coliforms was noted (p < 0.01) in faeces of group E compared with C. Pseudomonads and clostridiae were also significantly reduced (p < 0.001; p < 0.05) and slight decrease was also in CoNS and enterococci. On day 42, coliforms were still significantly reduced (p < 0.001) in faeces; slight decrease in CoPS and pseudomonads was noted. In the caecum, significant decrease in pseudomonads (p < 0.05) was noted on day 28; slight decrease in coliforms. In the appendix slight decrease in coliforms, pseudomonads was obtained on both days. PA was increased significantly in E on days 28, 42 (p < 0.001). Biochemical parameters were not influenced; nor were volatile fatty acids or lactic acid in the chymus. Nisin application did not evoke oxidative stress. In group E, an increase in average body weight gain (about 9.4 %) was noted. The villus height/crypt depth ratio was not influenced; that is, resorption surface and functionality of mucosa were not influenced.