Spondyloarthritis (SpA) is a group of chronic inflammatory diseases of the musculoskeletal system involving of the axial skeleton and extra-articular manifestations such as inflammatory bowel diseases. Some violations of the intestinal microbiome often occur during the course of spondyloarthritis. Also, intestinal dysbiosis can be enhanced by ongoing therapy. The aim of the study was to evaluate the effectiveness of combined therapy with nonsteroidal anti-inflammatory drugs (NSAIDs) and autoprobiotics supplementation.SpA patients treated with NSAID were divided into two groups: group A which took autoprobiotic based on indigenous culture of Enterococcus faecium, and group S which took only Supra medium, which is the basis used for making of autoprobiotic. Reducing of pain intensity, dyspeptic phenomena were observed to a greater extent in group A compared to group S. PCRRT testing revealed no significant changes in intestinal microbiocenosis in patients with SpA, except of a decrease in the Lactobacillus population, which was restored only in group A. A feature of the changes in group S was a decrease in the total bacterial mass, amounts of Bacteroides, Faecalibacterium, Enterobacter and expansion of Methanobrevibacter population. The tendency to restore the quantitative content of Lactobacillus, correlating with a decrease of IL-10 concentration, was found only in group A.In our study the effectiveness of enterococcal auprobiotic supplementation as an element of complex therapy of patient suffering from SpA has been proven. The use of an autoprobiotic leads to a decrease in the severity of the symptoms of the disease, the leveling of dyspeptic symptoms and microbiota disorders.