Congenital neuroectodermal defects are associated with meningitis that is unresponsive to conventional antibiotic therapy, recurrent bacterial meningitis, or meningitis due to an organism that is not usually the cause of this disease. Midthoracic dermoid and epidermoid cysts occur rarely and are easily overlooked. We report the case of a 13-month-old boy with meningitis that was unresponsive to antimicrobial therapy. We subsequently identified an intraspinal abscess, an infection due to Staphylococcus epidermidis, and a midthoracic dermoid cyst. We emphasize the need for clinicians to have a high index of suspicion and to make a careful physical examination when antibiotic treatment fails in patients with meningitis. We also provide a detailed anatomy of a midthoracic dermoid cyst and illustrate the usefulness of magnetic resonance imaging in preoperative diagnosis of congenital neuroectodermal defects.