The subependymal zone (SEZ), frequently named as adult subventricular zone (SVZ), is a niche of adult neural stem and progenitor cells that lines a large extension of the lateral ventricles of the brain. The majority of the studies do not analyze the SEZ throughout its entire extension. Instead, studies of cell populations within the SEZ typically focus their analysis on a narrow space between specific bregma coordinates that provides a perspective of only a small portion of the SEZ. We have previously proposed a standard division for the SEZ at the anterior-posterior and dorsal-ventral axes based on external brain anatomical hallmarks (Falcao et al., PLoS One 7:e38647, 2012). Herein, we describe in detail the procedure and a stereological approach that can be used to obtain an unbiased estimation of the SEZ cell proliferation under physiological and pathological conditions. This approach takes into consideration clear SEZ anatomical divisions, both on the anterior-posterior and dorsal-ventral axes, which will standardize future studies on the SEZ.