Entamoeba histolytica causes an estimated 100 000 deaths per year and is one of the leading causes of death among parasitic infections. Studies using E. histolytica-specific polymerase chain reaction identified that 13.8% of adults in a rural Mexican community and 11.2% of adults in central Vietnam are asymptomatically colonized. Such high incidents of asymptomatic infection suggest that only a minority of infections proceed to invasive disease. Understanding the mechanisms that underpin variable disease outcome will be critical in developing therapeutic strategies. In recent years there have been a plethora of gene expression profiling data documenting the transcriptome differences between virulent and non-virulent strains of E. histolytica as well as changes induced by external environmental changes or stimuli. While these studies have successfully identified co-regulated genes and potential virulence factors, there is still little known about the transcriptional mechanisms that induce the changes observed in this non-model organism. In this review, we have looked at how molecular technological advances have shaped our understanding of transcriptional regulation in amoeba and what we may expect from the application of powerful new techniques.