In this work the morphological and functional features of the small intestine mucosa depending on micriobiota of parietal small intestine in long term use antibiotic ceftriaxone and multiprobiotic or their co-administration were studied. Study was done on white laboratory rats, which were administrated daily with ceftriaxone antibiotic alone or along with multiprobiotic within 14 days, the autopsy was done on the 15th, 29th and 72nd days of the experiment. It was shown that antibiotic use caused morphological and functional state changes of the small intestine mucosa of rats, accompanied by hypertrophy of goblet cells and mast cell degranulation. The consequences of the antibiotic use remain even in periods after and not completely disappear at 29th and 72nd days of experiment. Morphofunctional changes of small intestinal mucosa constrained with changes in composition of intestinal microbiota that was characterized by the height of conditionally-pathogenic microbiota, in particular, Staphylococcus aureus and Candida. A chart of simultaneous application and abolition of multiprobiotic with an antibiotic is ineffective for the removal of negative consequences of introduction of antibiotic. Application of multiprobiotic together with an antibiotic and continuation of application of the multiprobiotic alone, or administration of multiprobiotic after antibiotic cessation are considerably more effective comparatively with the first mode and allows to decrease or fully remove violation of the functional state of mucous membrane of small intestine.