New memories initially persist in a labile state and require protein synthesis-dependent processes of consolidation for long-term manifestation. Using differential conditioning to linearly frequency-modulated tones (FMs) we have recently shown that post-training injections of protein synthesis inhibitors into the auditory cortex of Mongolian gerbils interfere with long-term memory for a number of days. Here, we have used rapamycin as a pharmacological tool to elucidate signalling pathways that control the synthesis of proteins required for persistent memory storage. In mammalian cells, inhibition of target of rapamycin (TOR)-mediated pathways was shown to block the translation of distinct classes of mRNAs. Bilateral infusions of rapamycin into the gerbil auditory cortex shortly after FM discrimination training did not impair the maintenance of the newly acquired memory trace for 24 h, but caused profound retention deficits at 48 h after injection. Control experiments showed that the amnesic action is rapamycin-dependent, confined to the context of memory formation, and suppressed by the antagonist FK506. These data indicate that, in the mammalian brain, activation of rapamycin-sensitive signalling pathways contributes to long-term consolidation of a cerebral cortex-dependent form of memory. Moreover, the finding that rapamycin-induced amnesia parallels only late effects of conventional protein synthesis inhibitors on FM discrimination memory implies that at least two different protein synthesis-dependent processes control memory formation. Both are activated during or shortly after learning. Whereas one process is required for the initial maintenance of memory for about one day the second one is involved in the regulation of its long-lasting persistence in conditioning to FMs.