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Celiac disease is an enteropathy characterized by malabsorption related with gluten intolerance and immune-mediated pathogenesis. It may manifest with gastrointestinal features like diarrhea, abdominal pain, weight loss, and anemia. Besides, it can manifest with various extraintestinal features like ataxia, neuropathy, stroke, or sometimes venous sinus thrombosis. Being of autoimmune origin, relation with systemic lupus erythematosus has also been reported. Herein, we present a rare case of a young patient with celiac disease who presented with fever, headache, and altered sensorium and was found to have meningitis with deep cerebral venous sinus thrombosis.