BackgroundObstructive sleep apnea (OSA) is a prevalent sleep disorder that is associated with structural brain damage and cognitive impairment. The hypothalamus plays a crucial role in regulating sleep and wakefulness. We aimed to evaluate hypothalamic subunit volumes in patients with OSA.MethodsWe enrolled 30 participants (15 patients with OSA and 15 healthy controls (HC)). Patients with OSA underwent complete overnight polysomnography (PSG) examination. All the participants underwent MRI. The hypothalamic subunit volumes were calculated using a segmentation technique that trained a 3D convolutional neural network.ResultsAlthough hypothalamus subunit volumes were comparable between the HC and OSA groups (lowest p = .395), significant negative correlations were found in OSA patients between BMI and whole left hypothalamus volume (R = –0.654, p = .008), as well as between BMI and left posterior volume (R = –0.556, p = .032). Furthermore, significant positive correlations were found between ESS and right anterior inferior volume (R = 0.548, p = .042), minimum SpO2 and the whole left hypothalamus (R = 0.551, p = .033), left tubular inferior volumes (R = 0.596, p = .019), and between the percentage of REM stage and left anterior inferior volume (R = 0.584, p = .022).ConclusionsWhile there were no notable differences in the hypothalamic subunit volumes between the OSA and HC groups, several important correlations were identified in the OSA group. These relationships suggest that factors related to sleep apnea severity could affect hypothalamic structure in patients.