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<em>Lactobacilli</em> are rod shaped gram positive bacteria that naturally colonize the human gastrointestinal and genitourinary tracts and occasionally cause disease in humans. <em>Lactobacillus</em> infections are found in patients who are immunocompromized or have severe comorbidities. We report <em>Lactobacillus</em> 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 <em>in vivo</em> 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 <em>Lactobacillus</em> endocarditis has not been reported in a pediatric patient with complex cyanotic congenital heart disease.