The biodiversity of Trypanosoma cruzi is one of the main factors complicating the understanding of its molecular epidemiology. As an alternative to classical genetic methods, investigators have used DNA-mediated transformation techniques to study this diversity. Recently, transient expression data were shown to correlate with the genetic data. This led investigators to speculate on a potential speciation within clonal populations of Trypanosoma cruzi. To further test the phylogenetic significance of transient expression analysis in Trypanosoma cruzi, multiple plasmids were used to drive the expression of a reporter gene in different parasite populations. In our study, population specific expression of the reporter gene was observed but the variability revealed by these transient expression assays was very large and did not follow the grouping of Trypanosoma cruzi populations in 2 lineages. In this report, we discuss some of the limitations of transient assays on such a diverse parasite.