Inflammatory bowel disease is an autoimmune disease with unclear etiology and characterized by recurrence and asymptomatic periods. Case Presentation This is an 11 year old male. Product of Gestation 4. No history of inbreeding or consanguinity. He starts with recurrent pulmonary infections of insidious course and with poor response to treatment. In addition to complicated pyelonephritis that requires hospitalization with a torpid course of response to antimicrobial treatment. During this period he presented bloody diarrhea, oral aphthae, perianal excoriations, asthenia and developed neutropenia, there was evidence of thickening of the intestinal wall and due to the risk of Fornier’s gangrene it was decided to perform a colostomy, a biopsy of the colon and small intestine was performed with results of colitis and unspecific proctitis. In addition, the patient presented deep pancytopenia with negative results for the search of neoplasias. Discussion Immune dysregulation in patients with inborn errors of immunity can present in a wide range of clinical presentations. The symptoms resemble the features of classic polygenic inflammatory bowel disease as seen in Crohn’s disease and ulcerative colitis. The current classification distinguishes subgroups of pediatric IBD by age, defining early-onset IBD as manifesting at less than 10 years of age, very early-onset IBD at less than six years of age and infantile IBD (<2 years), as well as neonatal IBD. Patients usually present with a complete phenotype of underlying immunodeficiencies, while another phenotype of patients present with enteropathies refractory to conventional therapies, adding that biopsy results are inconclusive and classical scoring systems are often not applicable, we bring this case of a 10 year old school boy, with an early onset presentation, to exemplify complexity of the diagnostic approach to the patient. It could be classified as an immune dysregulation syndrome, IUSI group IV classification, with colitis as the primary involvement.