A 10-year-old boy presented with an atypical non-febrile septic arthritis/osteomyelitis. He was unresponsive to routine antibiotic treatment with flucloxacillin/gentamicin as the pain and fluid collection increased. Synovial fluid cultures are negative and gram stain remained negative. Only after PCR/16S ribosomal bacterial DNA amplification a Fusobacterium nucleatum could be detected, and antibiotic therapy switched to clindamycin with rapid response. Septic osteomyelitis and arthritis are relatively rare but important infections in children needing prompt treatment, and should be considered when a child complaints about joint or bone pain without prior recent trauma. Skin bacteria are the most prevalent causative organisms, whereas Fusobacteria or other anaerobic, Gram-negative microorganisms are very seldom encountered. If cultures remain negative and the patients responds insufficiently to empiric treatment, PCR/16S ribosomal bacterial DNA amplification can be useful to detect the causative microorganisms.