This study focuses on developing new approaches to identify and quantify glycogen trophoblast cells in the placenta. Due to limitations with currently available methods, alternative markers for these cells are being explored. Here we report on one promising candidate, Aldh1a3, a gene that was recently shown to be expressed in the mouse placenta only in glycogen trophoblast cells and their progenitors. This study validates ALDH1A3 protein as glycogen trophoblast marker with high specificity when compared to CDKN1C. This marker will be useful for the isolation of the glycogen trophoblast subpopulation in order to examine its function in placental programming, and for understanding its role in pathological pregnancy models.