This chapter reviews the current understanding of the Toxoplasma transcriptome as it changes during the parasite intermediate life cycle. The chapter discusses the evidence that Toxoplasma possesses a similar repertoire of mechanisms to regulate transcription as observed in other well-studied eukaryotes, from yeast to multicellular animals. Given the importance of Toxoplasma infections to human populations, understanding developmental mechanisms initiated by sporozoites or bradyzoites leading to tissue cyst formation will be central to ultimately controlling transmission and chronic disease. Studies of Toxoplasma primary infections in animals and of sporozoite- and bradyzoite-infected cultures in vitro indicate that development initiated by either the sporozoite or bradyzoite stage is similar, and likely the consequence of a unified genetic program. Thus, defining the changes in gene expression that accompany this development pathway will be important to understand the underlying mechanisms responsible for toxoplasmosis caused by either route of infection.