Background: Transverse sinus (TS) is located anterior to the left atrium (LA) and almost posterior to the aortic root. Pericardial fat pad in transverse sinus adjacent to LAA is a rare condition that may resemble LAA thrombosis especially in suspected cases. Case presentation: A 60 years old woman with history of dyspnea on exertion and severe mitral stenosis was planned for percutaneous transvenous mitral commissurotomy (PTMC). In TEE imaging mass-like lesion near LAA was seen and was first thought to be LAA thrombosis. After more TEE angulations and 3D TEE the diagnosis of transverse sinus fat pad (TSFP) was confirmed. Conclusion: Along-side 2D imaging, 3D TEE we can better delineate the complex structure of LA and LAA.