A 48-year-old male patient had two episodes of fever, headache, confusion and seizures following an upper respiratory tract infection. Electroencephalography (EEG) revealed diffuse slowing of background activity. Plasma free carnitine and serum lipid levels were low; fecal fat content and serum antigliadin antibodies were elevated. Duodenal biopsy was compatible with gluten enteropathy. Symptoms improved after the patient was started on a gluten-free diet and carnitine replacement therapy. No recurrence was observed within a four-year follow-up. Carnitine deficiency in adulthood is unusual, and encephalopathy due to carnitine deficiency as a result of celiac disease has not been described previously.