Immune reconstitution inflammatory syndrome is a rare complication of the treatment of Whipple's disease. Here, we report the case of a 65-year-old man treated for Whipple's disease affecting the joints, with positive Tropheryma whipplei PCR in CSF, who developed fever and nodular eruption on the trunk, arms and face in association with biological inflammatory syndrome 10 days after initiation of antimicrobial treatment. Skin manifestations and the patient's general condition improved on corticosteroids (0.5mg/kg prednisone), but as steroids were gradually tapered, new nodules appeared below a prednisone dose of 10–15mg. One year after starting treatment, lumbar puncture showed asymptomatic meningitis with negative T. whipplei PCR results which had regressed spontaneously. Two years after the diagnosis, on prednisone 5mg daily and antimicrobial treatment, the patient had only transient, episodic nodular rash without fever or inflammatory syndrome.