Several neuroimaging studies underlined the importance of the amygdala and prefrontal brain structures (e.g. dorsolateral prefrontal cortex [DLPFC]) for the processing of emotional stimuli and for emotion regulation. Many studies used visual scenes or faces as emotion-inducing material, and there is evidence that negative or positive words activate emotion-processing brain regions in the same way. However, no study so far focused on the influence of subclinical measures of anxiety or depression on the neural processing of emotional words. In this fMRI-study, we therefore investigated brain activation to emotional words in relation to subclinical measures of trait anxiety and depression in a sample of 21 healthy subjects. We also assessed effects of subclinical anxiety and depression on amygdala-prefrontal coupling during negative (versus neutral) word reading. Both negative and positive words activated the amygdala, and negative-word processing revealed a positive correlation between amygdala activity and scores of trait anxiety and subclinical depression. During negative versus neutral word reading, subjects with high trait anxiety also showed a stronger functional coupling between left amygdala and left DLPFC. These results suggest a modulation of negative-word processing by subclinical depression and anxiety, as well as possible prefrontal compensatory processes during unintentional emotion regulation in subjects with higher trait anxiety.