Morbidity of inflammatory bowel diseases (IBD) has been increasing in children recently. The pathogenesis of these autoimmune diseases still remains unknown, so the therapy of IBD is mainly symptomatic. Chronic inflammation and applied treatment involve many complications, among which impaired bone mineralization is quite common. Great expectations arose when three cytokines were explored: osteoprotegerin (OPG), receptor activator of nuclear factor kB (RANK) and receptor activator of nuclear factor κB ligand (RANKL). These molecules were identified in many cells and play a key role in bone formation and resorption, as well as in the immune system. Due to increasing knowledge about these cytokines there are new possibilities for treatment of the diseases in which OPG, RANK and RANKL are engaged.