Objective Religious behaviors are considered as complex brain-based phenomena that may be associated with structural brain change. To identify the pattern of regional brain volume change in nuns, we investigated structural alterations in the brains of nuns using a fast processing automated segmentation method based on deep learning algorithms.Methods We retrospectively reviewed the medical records of the catholic sisters between the ages of 31 and 80 who are members of the charity of St. Vincent de Paul of Korea. A total of 193 asymptomatic subjects (86 nuns and 107 control subjects) received comprehensive health screening and underwent brain MRI scans. We compared cortical and sub-cortical volume between groups across multiple locations using our in-house U-Net++ deep learning-based automatic segmentation tool.Results Compared to the control group, the nun group displayed increased gray matter volume in the right lingual cortex, left isthmus-cingulate, posterior-cingulate, rostral-middle-frontal, superior-frontal, supramarginal, temporal-pole cortices, and bilateral pars-triangularis cortices after correction for multiple comparisons. On the other hand, the nun group showed reduced gray matter volume in the temporal and parietal regions relative to healthy controls.Conclusion Our study suggests that spiritual practice may affect brain structure, especially in several frontal regions involved in a higher level of insight function.