Our direct comparisons of relative transcript and protein abundance levels uncover a dynamic and complex picture of stage-specific gene and protein expression in P. falciparum. Particularly revealing are the insights into differentially expressed isoforms of some proteins that offer a glimpse of an almost bewildering complexity that may lie beneath corresponding RNA profiles and a deceptively simple appearance of overall protein abundance. Many of these isoform changes are fundamentally undetectable in transcript-level analyses and are invisible even to common protein-level investigations such as Western blotting and conventional high-throughput proteomics based on mass spectrometry. Our **data** reveal significant and distinct isoform changes for several proteins (for example, eIF4A, eIF5A, and HSP70-2) as the malaria parasites progress through the late stage of their intra-erythrocytic life cycle. The high reproducibility and temporal specificity of our observations strongly suggest that these changes are more than inconsequential fluctuations and that they represent biologically significant modifications. It is likely that many of these isoforms lead to different biological functionality of the cognate protein.