Arthralgias and spondyloarthropathies of the peripheral and axial joints are common in inflammatory bowel disease. Evidence for a strong association between these clinical manifestations and diseases of the joints has been provided by several clinical and epidemiological studies. Immunological studies have shown the presence of shared inflammatory cells both in the gut and the synovium in spondyloarthropathies. Genetic factors play a crucial role in the pathogenesis of spondyloarthropathies and inflammatory bowel disease. The role of the ubiquitous bacterial flora and pathogenic microorganisms present in the intestinal lumen may induce these joint diseases in patients with inflammatory bowel disease. In this review we will focus on the pathogenesis of spondyloarthropathies and arthralgia in patients suffering from inflammatory bowel disease. Based on preliminary clinical observations in patients with arthralgia and IBD, we put forward the hypothesis that probiotics may be helpful in the management of common extraintestinal manifestations such as arthralgia in patients with ulcerative colitis and Crohn's disease.