Malaria remains the most devastating parasitic disease worldwide, and is responsible each year for >500 million infections and between one million and two million deaths of children under five years of age. Plasmodium falciparum is the most prevalent and deadly malaria parasite of humans, and a huge amount of data about it is now publicly available following completion of its genome sequence, the complete transcriptome of its asexual blood stages and proteomic analyses of its different life stages. Thus, new computational approaches are needed to analyze these data to yield biologically meaningful results that can be validated experimentally and, hopefully, lead to alternative control strategies. In this article, we highlight the importance of new computational approaches in mining the malaria transcriptome of the intraerythrocytic developmental cycle of P. falciparum.