True Refractory Coeliac Disease (RCD) is being currently defined as persisting or recurring villous atrophy with crypt hyperplasia and increased intraepithelial lymphocytes in spite of a strict gluten free diet for more than 12 months or when severe persisting symptoms necessitate intervention independent of the duration of the dietary therapy. Currently two categories of RCD are being recognized: type I without aberrant T-cells and type II with aberrant T-cells detected by immunophenotyping by flowcytometric analysis or immunohistology of the intestinal mucosa. Establishing the diagnosis of RCD requires exclusion of other causes of villous atrophy and malignancies that may complicate coeliac disease. In contrast to patients with a high percentage of aberrant T cells, patients with RCD type I seem to profit from an immunosuppressive treatment. In cases of RCD II with persistent clinical symptoms and/or high percentage of aberrant T cells in intestinal biopsies in spite of a corticosteroid treatment, more aggressive therapeutic schemes should be considered. However, no therapy seems to be curative in RCD II. Cladribine (2-CDA) seems to have some role in the management of these patients. More recently, high dose chemotherapy followed by autologous stem cell transplantation has been used in patients resulting in a dramatic improvement in the clinical, laboratory, histopathological and immunological parameters. This review provides an overview of the currently available diagnostic and therapeutic methods in a complicated form of coeliac disease.