A small subset of coeliac disease (CD) patients experiences persisting or recurring symptoms despite strict adherence to a gluten-free diet (GFD). When other causes of villous atrophy have been excluded, these patients are referred to as refractory celiac disease (RCD) patients. RCD can be divided in two types based on the absence (type I) or presence (type II) of an, usually clonal, intraepithelial lymphocyte population with aberrant phenotype. RCDI usually runs a benign course and may be difficult to be differentiated from uncomplicated, slow responding CD. In contrast, RCDII can be defined as low-grade intraepithelial lymphoma and frequently transforms into an aggressive enteropathy associated T-cell lymphoma with dismal prognosis. This paper describes the clinical characteristics of RCDI and RCDII, diagnostic approach, and the latest insights in treatment options.