Common variable immunodeficiency (CVID) is an immunodeficiency disorder with a high incidence of gastrointestinal (GI) manifestations and an increased risk of gastric malignancy. We report a case of a CVID with mild anemia presenting with multiple GI manifestations: gastric low-grade dysplasia (LGD), enteropathy with villous atrophy, refractory Giardia infection, nodular lymphoid hyperplasia, and inflammatory bowel-like disease. The differential diagnosis with celiac sprue could be challenging because of CVID enteropathy with villous flattening. Gastric LGD in a patient with an increased risk for gastric malignancy makes the appropriate surveillance of gastric cancer in CVID challenging.