Longitudinal studies of biological domains in bipolar disorder (BD) are crucial in determining if such baseline changes are progressive. We reviewed reported studies of longitudinal brain structural/functional magnetic resonance imaging (MRI) and neuropsychological changes in BD through November 2012. Longitudinal brain structural MRI studies suggest cortical and subcortical abnormalities within networks subserving emotional regulation. There is evidence of neuroprogressive loss of gray matter volume in prefrontal and anterior cingulate cortex and the subgenual region, with less consistent findings in temporal and subcortical regions. Abnormal amygdala neurodevelopment is noted in adolescent onset BD and possible changes in hippocampus require further evaluation. The fewer reported longitudinal functional MRI studies suggest neurobiological changes in activation patterns involving fronto-limbic circuitry which relate to different illness phase and mood states. Early onset pediatric/adolescent BD may signify a more malignant course of illness in which extensive and executive neurocognitive deficits are found early and may persist, with some potential for improvement during remission and perhaps with treatment.