Although it has been shown that the basolateral amygdala (BLA) and the mediodorsal thalamus (MD) are critical for goal-directed instrumental performance, much remains unknown about the respective contributions of these structures to action selection. The current study assessed the effects of post-training BLA and MD lesions on several tests of instrumental action selection. We found that MD damage disrupted the influence of pavlovian cues over action selection but left intact rats' ability to select actions based on either the expected value or the discriminative stimulus properties of the outcome. In contrast, BLA lesions impaired performance on all three tests of action selection. Because both lesion types disrupted the influence of cues that signal reward over instrumental performance, we then investigated the involvement of these structures in pavlovian contingency learning using a task in which the predictive status of one of two cues is degraded by delivering its outcome noncontingently during the intertrial interval. As expected, the sham group selectively suppressed their conditioned approach performance to the cue that no longer signaled its outcome but continued to respond to the control stimulus. In contrast, both lesioned groups were impaired on this task. Interestingly, whereas the MD group displayed a nonspecific reduction in responding to both cues, the BLA group continued to show high levels of responding to both cues as if their performance was completely insensitive to this contingency manipulation. These findings demonstrate that the BLA and MD make important yet distinct contributions to instrumental action selection.