BACKGROUND Intermittent hypoxemia can cause changes in certain brain structures. However, in pediatric patients with obstructive sleep apnea (OSA) caused by adenotonsillar hypertrophy (ATH), there is only limited information on the effect of ATH-induced OSA on brain structures. This study sought to investigate alterations in amygdala and hippocampal volumes in children with OSA by ATH. MATERIAL AND METHODS Magnetic resonance imaging scans were applied in children who had ATH-induced OSA (ATH/OSA) and in healthy children. Amygdala and hippocampus volumes and adenoid sizes were measured on MRI volumetric images. The ratio of adenoid size/nasopharyngeal depth was used to describe the severity of adenoid hypertrophy. The clinical variables of the involved subjects were investigated. RESULTS One hundred ATH/OSA children and 100 healthy children without ATH/OSA participated in the study. The ATH/OSA children had higher amygdala volumes and amygdala/hippocampus volume ratios but lower hippocampus volumes than healthy controls, and the amygdala/hippocampus volume ratios were correlated with disease duration and hypoxemia conditions. However, our data showed that amygdala/hippocampus volume ratios were not correlated with the ratios of adenoid size/nasopharyngeal depth in the ATH/OSA children. In addition, the ratio of adenoid size/nasopharyngeal depths in ATH/OSA children was higher than that in healthy children in each subgroup based on the age of participants. CONCLUSIONS Compared to healthy controls, amygdala/hippocampus volume ratios are increased in children with ATH/OSA.