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Rationale: Sjogren's syndrome(SS) is a chronic autoimmune disease, which damages exocrine glands especially salivary and lacrimal glands, with xerostomia and xerophthalmia as common symptoms. Patient concerns: We report a case of a 49-year-old woman presented with pancytopenia. Her laboratory examinations lead us diagnose her as Sjogren's syndrome complicating pancytopenia. She had neurological symptoms during her treatment, which represent only 4.5% of Sjogren's syndrome complicating damage in nervous system. Diagnoses: Sjogren's syndrome complicating pancytopenia. Interventions: Dexamethasone (40mg QD for 4 days) and immunoglobulin (25g QD for 2 days) were administered for intensive treatment followed by oral methylprednisolone 40mg QD as maintenance treatment. Total glucosides of paeony 0.6g TID and danazol 0.2g BID per os were given. We also gave her Piperacillin-tazobactam and moxifloxacin for anti-infection and Fluconazole for anti-fungal therapy, as well as other supportive treatments. Outcomes: Follow-up of the patient observed the normalization of peripheral blood cell count, immunity indices and neurological examinations 6 months after discharge. Lessons: For patients presented with blood system abnormalities unilineage or multiple-lineage cytopenia in particular, history investigations and relevant examinations should be considered to exclude the existence of autoimmune diseases like Sjogren's syndrome.