Wernicke's encephalopathy is an acute neurolopsychiatric syndrome caused by thiamine deficiency, and classically presents with the triad of opthalmopathy, ataxia and altered mentality. Both prolonged total parenteral nutrition and reduced oral intake can induce Wernicke's encephalopathy during hematopoietic stem cell transplantation (HSCT). Although early treatment is important for recovery from Wernicke's encephalopathy, the vague symptoms and characteristics hinder early diagnosis. Furthermore, Wernicke's encephalopathy is not infrequent and can develop at any age during HSCT. Herein, we present two young patients developing Wernicke's encephalopathy during HSCT.