Whipple's endocarditis is a rare culture-negative endocarditis caused by Tropheryma whipplei, an intracellular gram-positive organism. Here, we present a case of a 60-year-old male who presented with transient ischemic attack and was found to have an aortic valve mass. Following successful excision, histopathologic assessment of the lesion was consistent with calcified amorphous aortic tumor, a rare non-neoplastic hamartomatous mass of the heart. However, 16s rRNA and 18s rRNA sequencing detected Tropheryma whipplei, and the diagnosis of Whipple's endocarditis was made.