Inflammatory Bowel Disease (IBD) includes Crohn’s Disease (CD), and Ulcerative Colitis (UC), the two main types of IBD. The IBD incidence is rising globally and among the young age. Endoscopy has a principal role in rating IBD mucosal lesions. Though, it is expensive and invasive. MicroRNAs could be included in regulation of particular genes and included in inflammation. Disorders in microRNAs levels might cause disease development. The objective of our study is to investigate the role of microRNA-16 and microRNA- 106a levels as indicators for diagnosis and assessing the IBD activity. The values of miR 16 and miR 106a were measured in plasma from 20 healthy volunteers (group I) and 40 UC patients (group II) and 40 CD patients (group III) by quantitative real time-PCR (qRT-PCR). Endoscopic severity index was calculated based on laboratory and endoscopic findings. Significant upregulation of miR 16 and miR 106a levels in group II and group III than group I. A positive correlation was demonstrated between both miR 16 and miR 106a with endoscopic severity index. ROC curves of miR 16 for detecting UC showed sensitivity and specificity of 92.5 % and 90 % particularly. ROC curves of miR 106a for differentiating active from inactive CD showed sensitivity and specificity of 90 % and 75 % particularly. both miR 16 and miR 106a could act as promising biomarkers of IBD diagnosis and assessing its activity aiding in its proper management.