The case of a patient who had a relapse of cerebral Whipple 's disease (WD) one year after discontinuation of a two-years' antibiotic treatment is reported. Neither the clinical course nor the results of magnetic resonance imaging (MRI) and routine examination of the cerebrospinal fluid (CSF) allowed the caring physician to predict the relapse. Retrospective analysis of serial specimens of CSF showed that slight CSF leucocytosis and intrathecal synthesis of IgA might have suggested persistence of infection. The decision to stop antibiotic therapy in cerebral WD is difficult, but evaluation of cell counts and of intrathecal synthesis of IgA may help in the decision. Some patients may need to take treatment indefinitely.