This is an open label mechanistic study to learn about the effect of Omalizumab on the clinical symptoms and immunohistological findings in established cases of EoE. The dosage for Omalizumab will be based on patient's body weight and baseline IgE level. Omalizumab will be administered subcutaneously every 2 or 4 weeks for total duration of 12 weeks. At enrollment, subjects will have EGD with biopsies performed to confirm diagnosis of EoE and further histologic analysis and special staining. Blood will be drawn for baseline testing and monthly for safety labs. At the end of the 12 week period, repeat endoscopy will be performed and biopsies taken to stain again for various mucosal markers like IgE, IL-13, IL-5 and Tryptase. The patients will be followed for response to therapy with regards to resolution of symptoms and improvement in histology findings on biopsy.