The present study examined the functional association of the amygdala and right ventral prefrontal cortex (PFC) during cognitive evaluation of facial expressions. A situation was created where emotional valence of the stimuli was unconsciously manipulated by using subliminal affective priming. Twelve healthy volunteers were asked to evaluate the facial expressions of a target face (500-ms duration) such as "anger", "neutral", or "happy". All target faces expressed relatively weak anger. Just before the presentation of the target face, a prime of three conditions of 35-ms duration, angry face, neutral face, and white blank was presented. The subjects could not consciously identify the primes in this procedure. Activity in the right amygdala was greater with subliminal presentation of the angry prime compared with subliminal presentation of a neutral face or white-blank stimuli. Most importantly, the degree of activation of the right amygdala was negatively correlated with that of the right ventral PFC only with the anger prime. Furthermore, activation of the amygdala was positively correlated with rate of judgment when the subjects recognized anger in the target faces. These results are discussed in terms of the functional association between the right PFC and the amygdala and its influence on cognitive processing.