Choline acetyltransferase mRNA and somal area increased selectively in the ventral nucleus basalis of rats trained that a tone signals immediate shock (i.e., predicts danger). Retrograde tracing showed the affected cells correspond to those that project to the auditory cortex. Behavior responses and mRNA increased significantly above those of control groups trained with the tone not signaling immediate shock. In one of those control groups, animals learned that the same tone signaled a shock-free period before shock. These animals showed a visibly decreased riboprobe and a trend toward smaller somal areas. These results implicate transcriptional regulation of choline acetyltransferase in long-term memory storage. Selective attention and inattention to the tone are possible components of memory encoded by the molecular changes reported here.