Coeliac disease is a chronic disease which occurs in about 1% of population. Malignant diseases are a severe complication of coeliac disease with a very poor prognosis. Most common malignancies associated with coeliac disease are non-Hodgkin lymphomas, small bowel adenocarcinoma and oesophageal carcinoma. It is not clear whether there is a joint aetiologic background between coeliac disease and malignancies, but it is presumed that the pathogenesis of these tumours in coeliac patients differs from the general population. The correlation between coeliac disease and breast cancer is specific, considering the lower incidence of this malignancy in coeliac patients. Although all types of non-Hodgkin lymphomas occur more often in coeliac patients, the risk is higher for T-cell lymphomas and intestinal lymphomas compared to B-cell and extraintestinal lymphomas. Enteropathy associated T-cell lymphoma is a rare and aggressive type of non-Hodgkin lymphoma, which shows the strongest correlation with coeliac disease. It is typically located in the small intestine and has a specific immunophenotype that distinguishes it from other extranodal lymphomas. Most commonly, it affects patients with type 2 refractory coeliac disease. Refractory coeliac disease is a non-reactive type of coeliac disease, in which the patient’s condition does not improve despite adherence to a gluten-free diet for more than a year. It is further divided into type 1 or 2, based on the whether the intraepithelial lymphocytes are phenotypically normal or abnormal. The immunophenotype of abnormal intraepithelial lymphocytes in type 2 shows a high resemblance to that in enteropathy associated T-cell lymphoma, therefore type 2 refractory coeliac disease is considered a premalignant lesion of this lymphoma. Diagnosing these patients tends to be very complicated, since most localizations of lesions are difficult to reach using standard diagnostic methods. Pathohistological analysis enables the final diagnosis. Diagnostic delay increases mortality as well as limits the therapeutic options. Coeliac disease is often discovered simultaneously with malignancy. Considering the fact that patients who adhere to a gluten-free diet do not have an increased risk of malignant diseases, and that early introduction of gluten-free diet reduces the risk of developing complications, early recognition and treatment of coeliac disease are crucial in improving survival of these patients.