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The brainstem, critical for motor function, autonomic regulation, and many neurocognitive functions, undergoes rapid development from the third trimester. Accordingly, we hypothesized it would be vulnerable to insult during this period, and that a difficult clinical course in the neonatal intensive care unit (NICU) would affect development, and be reflected through atypical shape. Our study population consisted of 66 neonates - all inpatients from the NICU at Victoria Hospital, London Health Sciences Centre, ON, Canada, of which 45 entered the final analysis. The cohort varied in gestational age (GA) and ranged from neurologically healthy to severely brain-injured. Structural MRI was used to quantify brainstem shape at term-equivalent age. From these images, brainstems were semi-automatically segmented and co-registered across subjects. The anterior-posterior dimensions on a sagittal maximum intensity projection were used as the basis for shape comparison. Factor analysis was used to summarize variation in shape and in clinical course to determine three shape factors and three clinical factors, and their relationship assessed using correlation. A factor driven by low GA and associated complications correlated with alterations in the posterior medulla, while a factor driven by complications independent of GA correlated with alterations in the midbrain. Additionally, single clinical measures most representative of their respective clinical factor (days in NICU; days on ventilation) predicted the changes. Thus, different clinical courses in the NICU may have different effects on the shape of the brainstem, and may mediate some of the distinct neurodevelopmental profiles observed in premature and brain-injured neonates.