Inflammatory bowel disease (IBD) is complex, multifactorial, polygenic diseases without a certain cure. Patients require lifelong surveillance, expensive treatments, risky surgeries, have increased cancer and other systemic disease risks. IBD consists of two groups as Ulcerative colitis (UC) and Crohn's disease (CD). Although pathogenesis of IBD is not clear, a dysregulated immune response to environmental factors (intestinal microbiota) develops in genetically susceptible individuals. As early diagnosis is hard, most patients are diagnosed at a later stage, however, they suffer from colon damage and lose the chance of early treatment. This thesis aimed to identify biomarkers that can analyze IBD patient risk profiles to control disease and reveal individuals at risk before the disease progresses further. Firstly, mutations in Turkish IBD patients were investigated in candidate regions of innate immunity (NOD2), adaptive immunity (IL-23R), and autophagy (ATG16L1) genes. Then, microbiota profiles of patients were revealed by NGS and qPCR. Finally, to identify relationship between mutations and microbiota, statistical analyses were performed with non-parametric methods. As a result of this study, Shannon index showed significant reduction of bacterial diversity in IBD patients versus the control group (p-value, 0.048). At the species level, relative abundance of F. prausnitzii decreased while abundance of E. coli increased in IBD patients. Significant relationship (p-value, 0.034) was found between rs11209026 genotype and F. prausnitzii reduction in CD but not in UC. In conclusion, converting significant observations into a molecular test kit can provide a molecular guide that helps gastroenterologists in planning personalized treatments in IBD patients.