The interstitial cells of Cajal have been identified in locations beyond the gastrointestinal tract, including the prostate, uterus and bladder. Indeed, there are reports of primary gastrointestinal stromal tumor (GIST) arising from each of these sites. We report the case of a 72-year old male who presented with benign prostatic hypertrophy and was diagnosed on retropubic prostatectomy as having a GIST. While the initial clinical and radiologic impression was that of a primary prostatic GIST, subsequent imaging ultimately revealed a small rectal extension as the source of the lesion. The purpose of our report is to highlight the need to assiduously rule-out gastrointestinal sources of GIST prior to making the diagnosis of primary prostatic GIST.