To survive within infected hosts, Toxoplasma gondii undergoes profound metabolic and morphological changes by differentiating into a cyst characterized by its resistance to the immune system and chemotherapy. The stimulus that triggers Toxoplasma encystation and the molecular mechanisms regulating the bradyzoite phenotype are still unknown. Here, we developed a differentiation method in conjunction with a selective and subtracted cDNA strategy devised to identify developmentally regulated transcripts. We isolated and analyzed 65 cDNA clones. In addition to bradyzoite specific cDNAs previously reported, we demonstrate that twelve genes are exclusively or preferentially transcribed in the encysted bradyzoite forms of T. gondii using semi-quantitative RT-PCR. Among cDNAs identified, are those encoding predicted homologues of chaperones (mitochondrial heat shock protein 60, T-complex protein 1), DNA-damage repair protein, phosphatidylinositol synthase, glucose-6-phosphate isomerase and enolase. The identification of these genes opens the way for further study of molecular mechanisms controlling gene expression during T. gondii encystation.