A central problem in neurobiology is the elucidation of the mechanisms that underlie left-right asymmetries in brain structure and function. Using a transcriptome screening approach, we found asymmetric gene expression patterns in the right when compared with the left hippocampal formation at postnatal days (P) 6, 9, and 60 in the rat. Of those genes that were differentially expressed, most were predominantly expressed in the right hippocampus at P6, whereas most were predominantly expressed in the left at P9 and P60. Real-time PCR analysis of genes associated with synaptic vesicle trafficking confirmed this pattern. At P6, 9 of 13 such genes were more robustly expressed in the right hippocampus, while only 1 gene was predominantly expressed in the left. Conversely, at P9, 5 of the 13 genes were more highly expressed in the left hippocampus and only 1 gene was predominantly expressed in the right. This pattern persisted at P60: eight genes were more robustly expressed in the left hippocampus, and the remaining five showed no hemispheric preference. These data demonstrate a pattern of early lateralized gene expression that is likely to underlie the establishment of functional asymmetry in the adult hippocampus.