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<p>Abstract</p> <p>Background</p> <p>The <it>var </it>multigene family encodes PfEMP1, which are expressed on the surface of infected erythrocytes and bind to various host endothelial receptors. Antigenic variation of PfEMP1 plays a key role in malaria pathogenesis, a process partially controlled at the level of <it>var </it>gene transcription. Transcriptional levels, throughout the intra-erythrocytic cycle, of 59 <it>var </it>genes of the NF54 clone were measured simultaneously by quantitative real-time PCR. The timing of <it>var </it>transcript abundance, the number of genes transcribed and whether transcripts were correctly spliced for protein expression were determined. Two parasite populations were studied; an unselected population of NF54 and a selected population, NF54VAR2CSA, to compare both the transcription of <it>var2csa </it>and the expression pattern of the corresponding protein.</p> <p>Methods</p> <p>Synchronized parasites were harvested at different time points along the 48 hours intra-erythrocytic cycle for extraction of RNA and for analysis of expression of variant surface antigens by flow cytometry. Total RNA from each parasite sample was extracted and cDNA synthesized. Quantitative real-time PCR was performed using gene-specific primers for all <it>var </it>genes. Samples for flow cytometry were labelled with rabbit IgG targeting DBL5ε of VAR2CSA and serum IgG from malaria-exposed men and pregnant women.</p> <p>Results</p> <p><it>var </it>transcripts were detected at all time points of the intra-erythrocytic cycle by quantitative real-time PCR, although transcription peaked in ring-stage parasites. There was no difference in the timing of appearance of group A, B or C transcripts, and dominant and subdominant <it>var </it>transcripts appeared to be correctly spliced at all time points. VAR2CSA appeared on the surface of infected erythrocytes 16 hours after invasion, consistent with previous studies of other PfEMP1. Transcription of the pseudogene <it>var1csa </it>could not be detected in NF54VAR2CSA cells.</p> <p>Conclusion</p> <p>The optimal sampling point for analysis of <it>var </it>transcripts using quantitative real-time PCR is the ring-stage, which is encouraging for the analysis of fresh clinical isolates. The data presented here indicate that there is no promiscuous transcription of <it>var </it>genes at the individual cell level and that it is possible to correlate dominant transcripts with adhesion phenotype and clinical markers of malaria severity.</p>