Opsoclonus-myoclonus syndrome (OMS) is a rare and debilitating disorder of unknown etiology affecting children and adults. Outcome is unfavourable; approximately 80% of children with OMS suffer from mild to severe neurological handicaps, mainly cognitive impairment. A standard therapy does not exist. Due to the possible immune-mediated mechanisms, treatment with steroids, ACTH, plasmapheresis and immunoglobulins can be successful. However, some children become steroid dependent and symptoms may reoccur after treatment has been finished. We present two girls with OMS, who had a prolonged clinical course lasting 4 and 9 years with many relapses. Both children developed symptoms around the age of two years. Diagnostic work-up to exclude neuroblastoma was negative. Several treatment modalities including oral steroids, dexamethasone pulses, immunoglobulin and cyclosporine were used without lasting success. In addition, cognitive impairment developed in both children. In order to prevent further clinical and mental deterioration, 6 pulses of cyclophosphamide in combination with dexamethasone pulses every 4 weeks were administered. Both children showed significant improvement of OMS symptoms. One girl is still symptom free 18 months after treatment, mild ataxia developed in the other after 12 months. Both children are mentally handicapped and in special need schools. We conclude that combination of cyclophosphamide pulses and dexamethasone pulse therapy is a therapeutic option even after a long clinical course to improve symptoms of OMS.