Introduction: Whipple’s disease is a chronic systemic infectious disorder with Tropheryma whipplei as an etiologic agent, occurring rarely and affecting numerous organs and systems. The variety of symptoms and a non-typical course make it difficult to establish a proper diagnosis. Purpose: In this study, etiopathogenesis, diagnostics and treatment of Whipple’s disease were presented based on the case report of 60-year-old man diagnosed with Whipple’s disease. Case presentation: Persistent diarrhoea with weight loss, lymphadenopathy in the abdominal cavity and moderate microcytic anemia predominated in the clinical picture. Diagnosis was put based on the clinical picture and macroscopic assessment of the small intestine and the presence of macrophages filled with a PAS-positive substance in the lamina propria. To deepen diagnostics, samples collected were assessed showing macrophages with the damaged mucosa, containing numerous elongated micro-organisms whose ultrastructure corresponded to Tropheryma whipplei. The patient’s clinical conditions improved after antibiotic therapy. Conclusions: It is vital to remember about Whipple’s disease in patients with chronic diseases due to a non-specific clinical picture and difficulties in establishing a proper diagnosis. When the disease is diagnosed unequivocally, proper and effective antibiotic therapy should be instituted immediately.