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In this study, we investigated alterations in the resting-state functional connectivity of the pre-frontal cortex in chronic heroin abusers using functional magnetic resonance imaging. We found that, compared with normal controls, in heroin abusers the left prefrontal cortex showed decreased functional connectivity with the left hippocampus, right anterior cingulate, left middle frontal gyrus, right middle frontal gyrus and right precuneus. However, the right prefrontal cortex showed decreased functional connectivity with the left orbital frontal cortex and the left middle frontal gyrus in chronic heroin abusers. These alterations of resting-state functional connectivity in the prefrontal cortices of heroin abusers suggest that their frontal executive neural network may be impaired, and that this may contribute to their continued heroin abuse and relapse after withdrawal.