Prenatal exposure to polychlorinated biphenyls (PCBs), persistent organic pollutants in food chains and environment, exerts negative effects on children's cognitive function. To study the long-term effects, we examined cognitive functions in the male children of women with substantial PCB exposure in Taiwan during 1978-1979 and investigated neural basis of cognitive function changes through structural magnetic resonance imaging (MRI) and functional MRI (fMRI), which included resting-state and task-activated fMRI with two paradigms: a 2-back task and a picture rotation task. Ten men aged 30.0+/-3.7 years with prenatal exposure to PCBs and 11 unexposed controls aged 28.1+/-3.1 years participated. Both groups had similar cognitive phenotypes and behavioral results. Structural MRI analysis results showed that the PCB group had increased cortical thickness over the right inferior parietal lobule. In the resting-state study, the PCB group showed alterations in the default mode network. During the tasks, the PCB group showed decreased task-induced deactivation signals in cognition-associated brain areas during the 2-back task but enhanced deactivations during the picture rotation task. This study demonstrated altered structural MRI as well as resting and task-related fMRI in men with prenatal PCB exposure, suggesting altered brain plasticity and compensatory neuropsychological performance.