Inflammatory bowel diseases (IBD), Crohn's Disease (CD) and Ulcerative Colitis (UC) are complex diseases showing genetic heterogeneity that arise with the interaction of the genetic and environmental agents. The prevalence of the cytokine gene polymorphism has different distributions in the various races of the world. In our study, 22 polymorphic regions of 13 different cytokine genes were evaluated in IBD patients in the Black Sea Region of Turkey. Sixty-nine IBD patients (18 with Crohn's disease and 51 with ulcerative colitis) and 100 healthy individuals as controls who lived in the Black Sea Region and whose clinical diagnoses were realized in Research Hospitals, were selected. DNA was isolated from the blood of the selected individuals and the analyses of the cytokine gene polymorphisms were determined with the method of PCR-SSP (sequence specific primer). When the patients were compared with the control group in terms of cytokine genes, significant changes were observed in the allelic frequencies of the diseased group compared to the healthy individuals thus implying a role of allelic frequencies in Crohn's disease and ulcerative colitis. We conclude that, the allelic changes arising at the genomic level in the cytokine gene polymorphisms in the Turkish population could make contributions to the clinic diagnosis of patients with IBD.