Celiac disease (CD) is an immune-mediated systemic condition triggered by dietary gluten occurring in genetically susceptible individuals. Our understanding of its numerous and varied clinical presentations has evolved over time, which has contributed to the incidence of CD increasing. In most cases, the diagnosis is readily established and patients promptly improve after commencing a gluten-free diet (GFD). However, in some, the diagnosis is not straightforward and presents a challenge to clinicians. Potential dilemmas include those with positive serology but normal histology, negative serology but abnormal duodenal mucosal histology, failure to respond to a GFD or response to a GFD without evidence of CD. In recent years, development of new assays and modifications to existing diagnostic algorithms for CD has also challenged the traditional role of small-bowel histology as critical in CD diagnosis.