To fill these knowledge gaps, in this study we aimed to (1) describe the expression of CD44, CD24, and ALDH1A1 in non-malignant breast tissue of cancer-free women; (2) assess the homogeneity of their expression across multiple cores pertaining to each woman; and (3) compare the immunohistochemical expression assessment for CD44, CD24, and ALDH1A1 by an expert pathologist with the automated image analysis results. Here, ALDH1A1 is linked to cancer.