In this case report, we describe a rare case of inter-atrial septal lipomatosis occasionally found in a PET-CT scan performed in an 81-year-old patient with a history of periprosthetic endocarditis post aortic prosthesis implantation. The patient reappeared in 2022 in the emergency department complaining of symptomatology of worsening asthenia, fever, and elevated inflammatory indices. He was hospitalized in Cardiology department on suspect of recurrence of endocarditis and underwent PET-CT examination that showed an increased metabolic finding at the interatrial septum. On possible suspicion of recurrence of infective endocarditis or cardiac tumor pathology, further diagnostic investigation by cardio-RM examination was requested. However, after radiologic consultation, the previous performed FDG-PET/TC examinations were re-evaluated and a misdiagnosed uptake at this level was revealed, which was assumed to be due to the endocarditis condition because of widespread uptake throughout the perivalvular area.