A 16-year-old female patient presented with recurrent pleuropericardial effusion, arthralgia, and atrioventricular (AV) block. Endomyocardial biopsy (EMB) of the right ventricle was performed for suspected myocarditis and revealed fibrous thickening of the arterial walls with luminal narrowing and immunoglobulin G (IgG) deposits in the perivascular areas. These findings suggested an immune complex disease, most likely systemic lupus erythematosus (SLE), and diagnosis was confirmed by serological and clinical changes. In patients with SLE, EMB is valuable in identifying intramural coronary disease and myocarditis; in our case, this procedure led to diagnosis of SLE.