Lactobacilli are rod shaped gram positive bacteria that naturally colonize the human gastrointestinal and genitourinary tracts and occasionally cause disease in humans. Lactobacillus infections are found in patients who are immunocompromized or have severe comorbidities. We report Lactobacillus endocarditis in a 17-year-old adolescent girl with cardiac prosthetic material following surgical correction for complex cyanotic congenital heart disease. Accurate identification of the organism can be delayed. Despite in vivo susceptibility to vancomycin, our patient clinically failed vancomycin therapy but ultimately responded to a six-week course of penicillin, in addition to a 4-week course of clindamycin and gentamicin. She recovered without the need for surgical intervention and has been symptom free for one year. Upon review of the literature, we found that Lactobacillus endocarditis has not been reported in a pediatric patient with complex cyanotic congenital heart disease.