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AE (alopecia and excoriation) is a mouse mutant phenotype that harbours a mutation in Gsdma3. Gsdma3 has been reported to regulate the development of skin and hair follicles. However, its role in the mammary glands has not been reported. In this study, we found that descendants bred from an AE mother died within 12 days after birth. Then, we found that the expression of Gsdma3 varied among the developmental stages of mammary glands. Subsequently, we systematically studied the phenotype of the mammary glands of AE and wild-type mice, revealing that the mammary glands were smaller in AE mice. The mammary glands of AE mice exhibited shorter ductal extension and less bifurcation. Immunohistochemistry staining indicated that the mammary glands of AE mice displayed more proliferating cells during puberty while secreting less β-casein during pregnancy and lactation. The lymph nodes in the mammary glands of the AE mice were larger and showed some pigmentation, suggesting that the immune reaction in the mammary glands was up-regulated. Under a transmission electron microscope, residual bodies were observed in the lymph nodes in the mammary glands of AE mice. Thus, we report a new function of Gsdma3 in regulating the development of mammary glands, and we demonstrate that the Gsdma3 gene may act as a suppressor of the immune reaction.