A 10-year-old girl with a lumbosacral myelomeningocele, managed with clean intermittent catheterization, presented with headache, vomiting, and lethargy. The cerebrospinal fluid (CSF) and urine cultures revealed Escherichia coli, documented to be the same subtype. The organisms were subtyped and the E. coli from both the urine and CSF were noted to be of the same strain. Management consisted of intravenous antibiotics and ultimate replacement of the ventriculoperitoneal shunt. Children with myelodysplasia and CSF shunts should be carefully monitored in a multidisciplinary fashion to anticipate, correctly diagnose, and treat CSF shunt infections associated with bacteriuria.