Coeliac disease (CD) is the most common cause of villous atrophy and is increasingly recognized. The majority of CD patients responds to a gluten-free diet (GFD). However, some patients experience persistence or recurrence of symptoms despite a GFD. These patients require further diagnostic workup. We describe a 62-year-old female with recurring symptoms attributed to refractory coeliac disease (RCD) type I. A 66-year-old patient with a similar history had aberrant intraepithelial lymphocytes characteristic for RCD type II in her duodenum. Furthermore, in a third CD patient described here, microscopic colitis was responsible for diarrhoea that persisted despite strict dietary adherence. Microscopic colitis is strongly associated with CD and should be considered in patients with this disease. On the basis of these three illustrative case studies, we discuss the causes of non-responsive CD and their respective diagnostic workup.