In this paper we report the results of gene expression profiling of C57Bl/6N mice hippocampus after trace fear conditioning (TFC), and the identification of genes regulated at early and late steps after conditioning. Several of the genes regulated at early steps following TFC appeared common to many training protocols. At later stages (2 and 6 h), most of the genes identified were different from those identified following other learning paradigms resulting in memory consolidation. At 6 h after training, few genes were upregulated in respect to the naïve condition, suggesting that many gene products have eventually to be downregulated to achieve stable synapses modification and memory formation. In conclusion, the results presented highlight a number of genes whose expression is specifically modified in the mouse hippocampus following TFC and demonstrate the specificity associated to different forms of conditioning.