Thrombosis of the inferior vena cava represents a significant percentage of all venous thrombosis that take place during the neonatal period, generally associated with risk factors such as the use of central venous catheter. The incidence of bacterial endocarditis in preterm infants is low. Objectives: To characterize the case of a preterm neonate with both conditions and to detail the disease changing spectrum in the neonatal population and its therapeutic possibilities. Case report: Premature newborn, 31 + 5 weeks of gestation who presented Enterococcus faecalis bacteremia, developed progressive thrombosis of the inferior vena cava and right atrium secondary to the use of umbilical venous catheter, with subsequent diagnosis of endocarditis. He was treated with anticoagulation with subcutaneous low molecular weight heparin. Given a favorable evolution, it was decided to continue the anticoagulation therapy for 4-6 weeks, and at the time of discharge, aspirin treatment was given. Conclusions: The preterm infant with infective endocarditis and intracardiac thrombus presents an interesting management dilemma. Treatment should be individualized according to the clinical evolution and safety profile of thrombolytic and/or anticoagulant agents. Availability and advantages of low molecular weight heparin have led to its use as an alternative treatment in neonates and infants with deep venous thrombosis.