BACKGROUND: Venous thromboembolism, including pulmonary embolism (PE), is a common disease identified in the emergency department that carries significant morbidity and mortality. In its most severe form, PE is fulminant and characterized by cardiac arrest and death. CASE REPORT: In the midst of risk-stratifying PE by using echocardiography to assess right ventricular function, thrombus-in-transit (free-floating clot in the right atrium or ventricle) may be seen. We present a case of a 49-year-old man diagnosed with an acute saddle PE who was incidentally found to have a thrombus-in-transit and patent foramen ovale and required open thrombectomy. Identification of these additional potentially life-threatening features was possible only due to our availability of risk-stratification resources, specifically bedside echocardiography. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Albeit rare, with a reported incidence estimated at 4%, the presence of thrombus-in-transit may change emergent clinical management. A multidisciplinary team of resources should be considered emergently as part of a hospital-based PE system of care.