Primary immune deficiency diseases (PIDs) are a heterogeneous group of inherited diseases characterized by variable genetic immune defects, conferring susceptibility to recurrent infections. They have a vast array of manifestations some of which involve the gastrointestinal and hepatobiliary systems. These complications can be the consequence of five different factors, namely, infection, autoimmune process, unregulated inflammation, malignancies and complications of therapeutic intervention. They may precede the PID diagnosis and, once developed, they pose high risk of morbidity. Untrained clinicians may treat these manifestations only at the level of their presentation, leaving the PIDs dangerously undiagnosed. In fact, early diagnosis of PIDs and accompanied gastrointestinal and hepatic complications clearly require appropriate treatment, and in-turn lead to an improved quality of life for the patient. To improve the awareness of gastroenterologists and related health care providers about these diseases, we have reviewed herein the complications of different PIDs focusing on gastrointestinal and hepatic manifestation.