Arthralgia and spondyloarthropathy of the peripheral and the axial joints are common in patients with inflammatory bowel diseases. Evidence for this association has been provided by clinical, epidemiologic, and immunologic studies confirming the presence of shared inflammatory pathways in gut and joint. Bacterial gut infections such as Salmonella typhimurium, Yersinia enterocolitica, Shigella, Campylobacter jejuni may induce reactive peripheral arthritis and 20% of these patients may develop chronic spondyloarthropathy. It is not certain that arthralgias in inflammatory bowel diseases are more frequent than in the general population but clinical articular manifestations compatible with spondyloarthropathy are present in 10% to 40% of patients with inflammatory bowel diseases. These enteropathic peripheral arthropathies without axial involvement are subdivided into a pauciarticular of large joints and a bilateral symmetrical polyarthropathy. The rationale and the challenges of using prebiotics, probiotics, and synbiotics in the management of patients with inflammatory bowel diseases with arthralgias and spondyloarthropathy are briefly reviewed. The rationale is based on the modulation of the ubiquitous intestinal flora by bacteria and their products that have been proven to be safe. The challenge is to find the "window of opportunity" to treat the evolutionary stage of joint inflammation. It seems to us that the major aim is not to treat patients who have a self-limited inflammatory joint disorder, but those patients with persistent arthralgias in an early phase of the disease. Seronegative and seropositive patients with early arthritis, before damage may occur, could be managed by this approach to improve the quality of life and to positively influence the natural course of the disease.