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Objective To report a case presented with atypical clinical and radiological appearance in the early stage and finally pathologically confirmed as chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids ( CLIPPERS) , aiming to improve the understanding of the disorder. Methods The clinical, imaging, laboratory and pathological features as well as treatment and prognosis of a pathologically confirmed CLIPPERS patient with repeated relapsing-remitting course and stepwise progression in nine years were retrospectively analyzed. Results There were five relapsing-remitting processes in total clinical course of nine years. The clinical and radiological appearance was atypical in the early stage. At the first attack, the patient presented with fever, headache, altered consciousness and epileptic seizure. In the following courses, the patient presented with ataxia, blurred vision and limb weakness. Brain MRI (2006-2009) showed multiple abnormal signals including supratentorial white matter, pons and cerebellum with patchy gadolinium enhancement. Treatment with steroids resulted in a favorable clinical and radiological improvement. The symptoms of this attack included limb weakness, blurred vision, dysdipsia and dysarthria. Physical examination showed cognitive dysfunction, multiple cranial nerves injuries and bilateral pyramidal signs. Brain MRI showed multiple abnormal signals involved pons and cerebellum predominantly as well as supratentorial white matter with punctate gadolinium enhancement peppering the pons and cerebellum. A characteristic predominantly T lymphocytic perivascular infiltration was seen on brain biopsy. Both the imaging and histological findings were consistent with the CLIPPERS features. High-dose steroids treatment was given and obvious clinical and radiological improvements were observed. After discharge, steroids were reduced slowly combined with the use of immunosuppressant to avoid relapse of the disorder. Conclusions There is heterogeneity in clinical manifestations of CLIPPERS with repeated relapsing-remitting course and imaging presentations are sometimes atypical in the early stage, which leads to the misdiagonsis and missed diagnosis. Distinctive pathology is the “gold standard” for definite diagnosis. The nosological position of CLIPPERS is still unclear. Repeated relapse-remitting leads to secondary cerebral atrophy and degeneration, with the risk of progressing to primary central nervous system lymphoma. Early and vigorous steroids treatment with continuing maintenance immunotherapy results in the decreased relapse and best long-term prognosis. The neurologist should strengthen the understanding of CLIPPERS for early correct diagnosis and treatment aiming to reduce the functional disability.