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Wholemount immunocytochemical staining was used to visualize basal and luminal epithelial-cell-specific cytokeratin and smooth muscle alpha-actin expression in the developing and adult rat prostate, in the pregnant rat mammary gland and adult rat salivary gland. The stained samples were examined using an Edge R400 3D microscope. Images were collected in both single-image and stereo-pair formats. Prostatic basal epithelial cells were found to have a cell body covering an area of 52-62 microns 2. The mean footprint size of basal cells was not significantly different between prostatic lobes. Basal epithelial cells were most dense in the anterior and most sparse in the ventral prostatic lobes. Basal epithelial cells had a large body with many processes, which spread around the duct and projected between luminal cells towards the lumen. These processes closely approached their counterparts from adjacent basal cells. In the developing prostate the differentiation of the basal cells from undifferentiated epithelial cords was observed at the region of ductal widening associated with canalization. Following castration prostatic basal epithelial cells became more closely packed, though the size of individual cells was not significantly changed. There was a two-to four-fold increase in basal cell density by 7 days after surgery. Most prostatic luminal cells were found to have hexagonal bases though some were pentagonal in shape. Luminal cells had a mean basal area of 50 microns 2. In the prostate immunocytochemical staining against smooth muscle alpha-actin revealed discrete bands of muscle surrounding individual prostatic ducts. In the mammary and salivary glands the epithelium was organized into an alveolar arrangement. In the salivary gland a single basal epithelial cell covered the top of each alveolus with processes arranged down the side of the structure. In the mammary gland several basal cells were draped over each alveolus. The mammary and salivary gland basal cells expressed smooth muscle alpha-actin, indicating their myoepithelial phenotype. The organization of the mammary and salivary gland basal cells placed them in an ideal position to squeeze the alveolar structures.