Infection after implantation of ventriculo-peritoneal shunts is associated with significant morbidity and mortality. We describe a 9-year-old girl with Propionibacterium acnes shunt infection with negative cerebrospinal fluid cultures, diagnosed by broad-range 16S-rRNA gene polymerase chain reaction. This case supports the use of this molecular diagnostic technique in shunt infections, where the offending pathogens are difficult to culture using traditional methods.