The data in the present article are related to the previous article entitled "Coxsackievirus and adenovirus receptor-positive cells compose the putative stem/progenitor cell niches in the marginal cell layer and parenchyma of the rat anterior pituitary" (Chen et al., 2013). The data describe the characteristic localization of coxsackievirus and adenovirus receptor (CAR), a junctional adhesion molecule involved in the regulation of cell-cell interactions, migration, proliferation, and growth (Coyne and Bergelson, 2005, Matthaus et al., 2017, Raschperger et al., 2006, Schiestl and Gietz, 1989) and in the stem/progenitor cell niche in the embryonic rat pituitary gland (Chen et al., 2013, Yoshida et al., 2016). Immunohistochemical analyses of CAR showed frequent colocalization with SOX2 in the embryonic rat brain, except for choroid plexus cells. CAR showed distinct apical and basolateral polarity. These data contribute to our understanding of prenatal brain development.