Formerly considered a rare disorder, eosinophilic esophagitis (EoE) has emerged as a leading cause of feeding problems in children and an increasingly recognized cause of dysphagia and food impaction in adults. Our understanding of EoE and its complex interplay with gastro-esophageal reflux disease (GERD) has evolved over the past decade and culminated in the introduction of proton pump inhibitor (PPI) responsive EoE as a distinct entity which has added to this complexity. It is now clear that this entity is on the same spectrum as the original EoE, and that PPIs should be considered as part of treatment protocol and should not be recommended as a diagnostic tool. As such, removing the PPI trial from the diagnostic algorithm has been encouraged recently. Recent guidelines and reviews thoroughly address various aspects in EoE pathogenesis and diagnostic workup as well as management endpoints, treatment options and novel therapies. However, despite the recent extensive study and the advances in our knowledge of this disease, unmet needs and pitfalls in diagnostic workup and management of these patients are still to be clarified and will be under focus in this review.