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Neuroimaging studies of adults with bipolar disorder (BD) have identified several BD subtype distinctions, including greater deficits in prefrontal gray matter volumes in BD-I (bipolar I disorder) compared to BD-II (bipolar II disorder). We sought to investigate BD subtype differences in brain structure among adolescents and young adults.Forty-four youth with BD (14 BD-I, 16 BD-II, and 14 BD-not otherwise specified [NOS], mean age 17) underwent 3T-MRI and images were analyzed using FreeSurfer software. Cortical volume and thickness were analyzed for region of interest (ROI): ventrolateral prefrontal cortex, ventromedial prefrontal cortex, anterior cingulate cortex (ACC), subgenual cingulate cortex, and amygdala, controlling for age, sex, and total intracranial volume. ROIs were selected as found to be implicated in BD in prior studies. A whole brain vertex-wise exploratory analysis was also performed. Uncorrected results are presented.There were group differences in ACC thickness (F = 3.88, p = 0.03, ηThis study found reduced cortical thickness for youth with BD-II, relative to BD-I, in regions associated with cognitive control. Further neurostructural differences between subtypes may emerge later during the course of illness.