Malakoplakia is a rare chronic granulomatous disease that may affect many organs, the genitourinary tact being the most common site. The second most common site is gastrointestinal tract. Here, we present a case of a 72year old immunocompetent female with a past history of Barrett’s oesophagus who underwent upper and lower GI endoscopy. Apart from three rectal polyps, the endoscopic examination was normal. Histological examination confirmed polypoid mucosa with malakoplakia manifested by the presence of characteristic Michaelis-Gutmann bodies. This is a rare case of isolated rectal polyposis with malakoplakia diagnosed on endoscopic specimens. Most of the reported cases of rectal malakoplakia have shown an association with systemic disease and/or colorectal carcinoma. Furthermore, there has been strong association with immunodeficiency or infective aetiologies.