Whipple’s disease is a rare systemic infectious disease caused by the actinobacterium Tropheryma whipplei. Spondylodiscitis is an extremely rare manifestation of the infection and has previously been described in only three case reports. We present a 55-year-old man with persistent lumbago and signs of systemic illness, but without any gastrointestinal symptoms or arthralgia. The signal response in the lumbar spine in magnetic resonance tomography, both native and after intravenous gadolinium administration, was compatible with spondylodiscitis at the L4/L5 level. Culture of a specimen obtained by radiographically guided disc puncture and repeated blood cultures remained sterile. Tropheryma whipplei was detected by PCR amplification in material obtained from the disc specimen, from a biopsy of the terminal ileum and from the stool. The histology of duodenum, terminal ileum, colon and disc material was normal and, in particular, showed no PAS-positive inclusions in macrophages. Long-term antibiotic treatment with sulphamethoxazole and trimethoprim was successful, with marked improvement of the low back pain and normalisation of the systemic inflammatory signs. The possibility of Whipple’s disease must be suspected in the case of a ‘culture-negative’ spondylodiscitis even if there are no gastrointestinal symptoms and no arthralgia present.