The genome of the kinetoplastid parasite Trypanosoma cruzi, causative agent of Chagas disease, was published nine years ago, yet a systematic and comprehensive analysis of the transcriptomes of the parasite and the human host has not been conducted. The parasite responds rapidly to transmission between arthropod vectors and mammalian hosts by undergoing complex cellular differentiation processes that are not well understood. In this study, we generated the first transcriptome map for both T. cruzi and infected human host cells across the infection cycle including time points of 4, 6, 12, 24, 48 and 72 hours post invasion with the next generation RNA sequencing technology (RNA-Seq). We also captured the transcriptome of the parasite in its bloodstream form (trypomastigote) and its replicative form inside insect vector (epimastigote). We successfully mapped transcribed regions for the pathogen at single nucleotide resolution on a genomic scale and characterized the RNA processing (trans-splicing and polyadenylation) events across its various developmental stages. Here we report the prevalent heterogeneity of RNA processing sites across the genome. We also note the preference of different primary sites in various developmental stages presenting as a potential and interesting approach of posttranscriptional regulation, which may hypothetically contribute to the survival of the parasite across different environments. Our work has significantly enhanced the current genome annotation of T. cruzi. In addition, using the T. cruzi and human genome sequence as reference, we explored these data with informatics tools to identify genes with significant regulation and successfully profiled gene expressions from both species simultaneously. We examined the subsets of differentially expressed genes both in the parasite and the host cell over the course of the infection to understand the mechanisms of invasion and intracellular survival strategy as well as host-pathogen interactions. T. cruzi genes that were significantly regulated during the infection process might present as new targets for drug development, whereas human genes that were significantly regulated might signal the immunoinflammatory response triggered by the manipulation of the parasite. Furthermore, we investigated the gene expression patterns of T. cruzi across its different developmental stages, clustered gene with similar patterns, and identified possible sequence motifs in coexpressed gene clusters.