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Diagnosing sepsis at postmortem is challenging. With respect to meningococcal sepsis, the postmortem microbiological identification of Neisseria meningitidis is nearly always due to true infection, including in cases of decomposition. Previous case series and case reports were able to isolate N. meningitidis in vitreous humor in adult deaths from meningococcal sepsis when blood and/or cerebrospinal fluid was unavailable. It was suggested that vitreous humor polymerase chain reaction (PCR) may be useful in the diagnosis of meningococcal sepsis. We describe a fatal case of meningococcal sepsis in a 5-month-old infant where N. meningitidis was detected in vitreous humor, cerebrospinal fluid, and blood through PCR. The presented case report gives further evidence in the potential use of vitreous PCR analysis in suspected meningococcal sepsis, particularly in the pediatric population.