Signal transduction plays a key role in regulating important functions in both multicellular and unicellular organisms and largely controls the manner in which cells respond to stimuli. Signal transduction pathways coordinate the functions in different type of cells in animals and control the growth and differentiation in unicellular organisms. Intracellular signal transduction pathways are largely activated by second messenger molecules. Trypanosoma cruzi has a complex life cycle involving four morphogenetic stages with various second messenger systems able to regulate its growth and differentiation. Signal transduction often alters the status of phosphorylation in target proteins and thus alters the activities of these proteins. In this review, two major signal transduction pathways, cyclic AMP-dependent pathway and mitogen-activated protein kinase pathway, are discussed. Protein phosphatases are also discussed due to their importance in dephosphorylating target proteins and terminating signal transduction. Understanding of the unique pathways in this pathogen may lead to the development of novel therapeutic agents.