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To investigate the relationship between blood glucose fluctuation and brain damage in the hypoglycemia neonates.A retrospective study including all neonates hospitalized due to hypoglycemia from September 2013 to August 2016 was performed. All the 58 hypoglycemia infants were divided into two groups—the brain-damaged group and the nonbrain-damaged group, according to head magnetic resonance imaging and/or amplitude-integrated electroencephalogram. Relationship between glucose variability and brain damage and whether these variation indexes could act as early indicators for hypoglycemic brain damage were investigated.Of the 13 brain-damaged cases, the lowest blood glucose (LBG) level was lower, while duration of hypoglycemia was longer compared with the 45 nonbrain-damaged cases (p < 0.001). The largest amplitude of glycemic excursions, standard deviation of blood glucose, and mean amplitude of glycemic excursions (MAGE) of the brain-damaged group were higher (p < 0.001). Under receiver-operating characteristic curve, values of area under the curve of MAGE were 0.892, duration of hypoglycemia was 0.921, and LBG was 0.109 (p < 0.0001).Brain damage of the hypoglycemia neonates relates not only with LBG and duration of hypoglycemia but also with the blood glucose variation indexes; MAGE and duration of hypoglycemia could act as predictors for brain damage.