Children with long-standing obstructive sleep apnea (OSA) show evidence of neural injury and functional deficits in behavioral and cognitive regulatory brain regions that are reflected in symptoms of altered cognitive performance and behaviors. While we earlier showed reduced gray matter volume and increased and reduced regional cortical thicknesses, such structural changes give little indication of the underlying pathology. Brain tissue integrity in pediatric OSA subjects can reflect the nature and extent of injury or structural adaptation, and can be assessed by entropy tissue texture, a measure of local changes in signal intensity patterns from high-resolution magnetic resonance images. We collected high-resolution T1-weighted magnetic resonance images from 10 pediatric OSA (age, 7.9 ± 1.1 years; apnea-hypopnea-index, 8.8 ± 3.0 events/hour; body-mass-index, 20 ± 6.7 kg/m2; 7 male) and 8 healthy controls (age, 8.8 ± 1.6 years; body-mass-index, 19.6 ± 5.9 kg/m2; 5 female). Images were bias-corrected and entropy maps calculated, individual maps were normalized to a common space, smoothed, and compared between groups (ANCOVA; covariates: age, gender; SPM12, uncorrected-threshold p < 0.005). No significant differences in age (p = .48), gender (p = .59), or body-mass-index (p = .63) emerged between groups. In OSA children, several brain sites including the pre-frontal cortex, middle and posterior corpus callosum, thalamus, hippocampus, and cerebellar areas showed reduced entropy values, indicating tissue changes suggestive of acute insults. No regions showed higher entropy values in OSA. Children suffering from OSA display predominantly acute tissue injury in neural regions principally localized within autonomic, respiratory, cognitive, and neuropsychologic control, functions that correspond to previously-reported comorbidities associated with OSA. A range of acute processes, including hypoxia/re-oxygenation, repeated arousals, and episodic hypercarbia, may have contributed to regional brain tissue integrity changes in pediatric OSA.