Congenital cardiac disease is recognized as a major predisposing substrate for infective endocarditis. We present three cases of unanticipated intraoperative discovery of vegetations in patients with congenital cardiac malformations without preoperative clinical, laboratory or echocardiographic evidence of infective endocarditis, and their successful treatment. The relevant literature is reviewed, with emphasis of the need to maintain a high index of suspicion for the presence of endocarditis during repair of congenital cardiac lesions.