16S rDNA polymerase chain reaction (PCR) in the diagnosis of fastidious organisms is becoming increasingly commonplace. We present the case of a child admitted to an acute paediatric unit of a university teaching hospital with otorrhoea, torticollis, and cervical lymphadenopathy. Examination revealed hepatosplenomegaly associated with pancytopenia. Radiological imaging confirmed a retropharyngeal abscess, bilateral mastoiditis, cerebellar lesions, and venous sinus thrombosis. Swabs of aural discharge grew anaerobes. Drainage of the retropharyngeal abscess and bilateral mastoidectomy were performed. Bone marrow aspiration was initially suspicious of acute leukaemia prompting further investigations, but cytogenetic analysis ruled out this diagnosis and changes were attributed to severe sepsis. Following 27 days of intravenous antibiotics and after clinical improvement, clindamycin was started. Intraoperative pus yielded no significant pathogens. A 16S rDNA PCR confirmed Fusobacterium necrophorum. The boy was discharged on a 6 week course of oral clindamycin.