The molecular biology of the clinically silent pre-erythrocytic stages of mammalian Plasmodium spp, composed of both the sporozoite and liver stages, has remained largely uncharacterized. Improved understanding of the biological processes required for progression through the pre-erythrocytic stages could lead to the identification of novel drug and vaccine targets. To gain insights into the molecular events that occur during the pre-erythrocytic stages of Plasmodium, comparative transcriptional analysis was performed on radiation attenuated sporozoites (RAS), wild type sporozoites (wtSPZ) and liver stage parasites collected either 24 hours (24hrLS) or 48 hours (48hrLS) after mice were infected with Plasmodium yoelii. Our results revealed 1100 Plasmodium genes that were differentially expressed in one or more constituents of the pre-erythrocytic stages relative to the mixed blood stages. Overall, the transcriptional profile of P. yoelii gradually became more similar to the mixed blood stages as pre-erythrocytic stage development progressed into the mature liver stage schizont. The transcriptional profiles of RAS and wtSPZ were found to be nearly identical. Likewise, the transcriptional profile of 24hrLS was very similar to that of the 48hrLS parasites. The largest differences in gene expression were observed when comparing wtSPZ or RAS to either of the liver stage samples. Further characterization of the differentially expressed genes identified in this study could help elucidate the biological mechanisms employed by Plasmodium during the pre-erythrocytic stages.