A nine day infant with Down syndrome and congenital heart disease is presented in whom the course of neonatal sepsis was complicated by the presence of difficult to diagnose pathological masses in the right ventricle. The etiology of pathological masses was difficult to establish in survival investigations. Histopathological examinations revealed the presence of thrombus in the right heart and foci of granulation on a muscle of right ventricle outflow, probably after a septic embolus.