Up to 5% of patients with newly diagnosed celiac disease have negative serology. Although seronegative celiac, is the most common cause for villous atrophy, there are other differential diagnoses that should be ruled out when we find villous blunting without positive serology for celiac disease. The aetiologies are usually divided into 5 categories: immune-mediated, infectious, iatrogenic, inflammatory and infiltrative. We hereby report a case of 39 years old male, with end-stage renal failure and pancreatic insufficiency. He was treated with peritoneal dialysis and was a candidate for combined kidney-pancreas transplantation. Hyperphosphatemia is a common complication in patients with end-stage renal disease. In order to reduce his serum phosphate levels, he was treated with a high dose of lanthanum carbonate, one of the most effective and safe non-calcium-based phosphate binders. During weight loss investigation, he underwent gastroscopy that demonstrated duodenal denudated mucosa with villous blunting. Biopsy showed complete villous atrophy and accumulation of foreign material in mucosal histiocytes. Von Kossa staining, that was performed, emphasized the depositions of the foreign material that has been identified as lanthanum. Consequently, the treatment with lanthanum was stopped and replaced by another phosphate binder. This case illustrates a rare differential diagnosis of villous atrophy typical for end-stage renal disease patients, that can be categorized as an iatrogenic and infiltrative aetiology for villous atrophy. Since the long-term consequences of lanthanum deposition in tissue are unknown, this case also emphasizes the need for a multidisciplinary approach for treating dialysis patients, in order to understand which phosphate binder was provided.