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We describe a young man who initially presented with stroke and febrile illness. He was eventually diagnosed with Tropheryma whipplei endocarditis. This is a very rare condition and to the best of our knowledge, this is the first documented case of T. whipplei endocarditis in Australia and New Zealand regions. This report aims to increase awareness of clinicians of this very rare but potentially treatable condition. It is reasonable to exclude T. whipplei endocarditis when dealing with high-risk patients who are suspected for “culture-negative” endocarditis.