The isolation of Chryseobacterium indologenes as a causative micro-organism in human diseases is rare. Risk factors for infections caused by this pathogen include very young and very old age, indwelling devices, immune suppression and recent use of broad-spectrum antibiotics. Most cases suffer from bacteraemia or nosocomial pneumonia, whilst infection of the central nervous system (CNS) is extremely rare. We present a term-born infant diagnosed prenatally with holoprosencephaly and obstructive hydrocephalus, requiring post-natal ventriculoperitoneal shunt insertion. At 6 weeks of age, he suffered from Escherichia coli meningitis, showing satisfactory clinical response with antimicrobial therapy. Aged 11 months, he suffered from hyper-drainage syndrome, resulting in the removal of the shunt system. He represented 11 days post-operatively, with low-grade fever, irritability and cerebrospinal fluid (CSF) leakage. C. indologenes from CSF was isolated and antimicrobial therapy with ceftazidime and trimethoprim-sulfamethoxazole for 3 weeks resulted in good clinical response. This is the first documented community-acquired CNS infection due to C. indologenes in an infant without concomitant indwelling device or previous antibiotic pressure.