The questions of whether and how indiscriminate drug-related stimuli could influence drug-users are important to our understanding of addictive behavior, but the answers are still inconclusive. In the present preliminary functional magnetic resonance imaging study using a backward masking paradigm, the effect of indiscriminate smoking-related stimuli on 10 smokers and 10 nonsmokers was examined. The BOLD response showed a significant reduction (P = 0.001) in the right amygdala of smokers when they viewed but did not perceive masked smoking-related stimuli, while no significant differences were found in the nonsmoker group. More voxels in anterior cingulate cortex were negatively correlated with the amygdala during the masked smoking-related picture condition in smokers but not in nonsmokers, whereas more positively correlated voxels were observed during the masked neutral condition. The BOLD response in drug-users indicates the amygdala responds to drug-related stimuli that are below the perceptual threshold. The functional connectivity data suggest a functional interaction between the amygdala and the anterior cingulate cortex when drug users view 33 ms back-masked drug-related stimuli. This observation suggests that the amygdala plays an important role in the indiscriminate drug-related cue process.