The Interleukin-23 signalling pathway is important for the differentiation of TH17 lymphocytes and is involved in the pathogenesis of Inflammatory bowel disease. Polymorphisms in the IL-23 receptor gene were previously found to be associated with Inflammatory bowel disease in various populations. The aim of this study was to determine whether the specific rs11209026 and rs7530511 single-nucleotide polymorphisms in the Interleukin-23 receptor gene are associated with Crohn's disease and ulcerative colitis in a Croatian patient population. A total of 50 patients with Crohn's disease and 93 patients with ulcerative colitis, as well as 99 healthy control subjects were included in the study. The results determined a significantly higher occurrence of rs11209026 in control group compared to patients with inflammatory bowel disease, suggesting a protective effect of this polymorphism. The rs11209026 variant was strongly associated with Crohn's disease, but it was absent in ulcerative colitis. However, there was no significant association between the rs7530511 polymorphism with either ulcerative colitis or Crohn's disease. Associations presented in this study give potentially important insight into the roles of specific Interleukin-23 receptor polymorphisms in Crohn's disease pathogenesis in the Croatian population.