Embryonic stem cells are considered to be a good in vitro tool to study the induction of various cell types including cardiomyocytes; however, induction of the pharyngeal endoderm (PE), the underlying heart-forming region, in vivo has been scarcely reported. In the present study, we found that many PE-related genes, such as Pax1, Pax9, Six1, and Tbx1, were up-regulated in cardiomyocyte-rich embryoid bodies (EBs). The third pouch-related genes including Hoxa3, Foxn1, and Aire, which are crucial for thymus development and function, were also detected in later stages. Nkx2.5, a cardiac transcription factor gene, is known to be transiently expressed in the PE. By crossing Nkx2.5-Cre mice with Cre-dependent EGFP reporter mice, we found that Nkx2.5(+) lineage exclusively contributed to thymic epithelial cell development, followed by thymus development. Gene expression analysis using Nkx2.5-EGFP ES cells also revealed that PE-related mRNAs were specifically enriched in the transiently appearing E-cadherin(+)Nkx2.5(+) cell fraction. Interestingly, the EB-derived cells were found capable of supporting T-cell differentiation to CD4 or CD8 double-positive cells in a reaggregation organ culture in vitro. Our results suggest that EBs contain cells that resemble third pharyngeal pouch endoderm and confer a thymus-like microenvironment.