INTRODUCTION: Malakoplakia is an uncommon inflammatory condition usually affecting the genitourinary tract, which has been associated with infections, tumours and immunocompromised states. CASE PRESENTATION: We report a case of malakoplakia in the appendix of a 61-year-old man with a long-standing history of ulcerative colitis. Clinically and macroscopically malakoplakia can simulate tumours or abscesses and can cause diagnostic difficulties. Histologically malakoplakia in the gastrointestinal tract must be differentiated from Whipple disease, other infectious and noninfectious granulomatous disorders and histiocyte storage diseases. To the best of our knowledge, this is the first case of malakoplakia of the appendix reported in association with ulcerative colitis and the sixth reported case of malakoplakia of the appendix in the literature. Although the underlying disease in our case was ulcerative colitis, the malakoplakia was limited to the appendix. CONCLUSION: The significance of this finding is not clear but we feel that this was a localised manifestation of the underlying immunosuppressive state. Ulcerative colitis and treatment with steroids may make a patient immunosuppressive and the local and systemic change in the immunity may facilitate the proliferation of the organisms and modify the phagocytic abilities of the macrophages.