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Approach-avoidance conflict arises when the drives to pursue reward and avoid harm are incompatible. Previous neuroimaging studies of approach-avoidance conflict have shown large variability in reported neuroanatomical correlates. These prior studies have generally neglected to account for potential sources of variability, such as individual differences in choice preferences and modeling of hemodynamic response during conflict. In the present study, we controlled for these limitations using a hierarchical Bayesian model (HBM). This enabled us to measure participant-specific per-trial estimates of conflict during an approach-avoidance task. We also employed a variable epoch method to identify brain structures specifically sensitive to conflict. In a sample of 28 human participants, we found that only a limited set of brain structures [inferior frontal gyrus (IFG), right dorsolateral prefrontal cortex (dlPFC), and right pre-supplementary motor area (pre-SMA)] are specifically correlated with approach-avoidance conflict. These findings suggest that controlling for previous sources of variability increases the specificity of the neuroanatomical correlates of approach-avoidance conflict.