Decay‐accelerating factor (DAF, CD55) is a glycosylphosphatidylinositol (GPI)‐linked membrane inhibitor of complement activation. While human and other mammalian species contain only one DAF gene, two distinct DAF genes, referred to as GPI‐DAF and transmembrane (TM)‐DAF, respectively, have been identified in the mouse. Using several independently generated monoclonal and polyclonal antibodies, either with dual or single specificity for GPI‐DAF and TM‐DAF gene products, we have examined the expression of the two DAF genes in tissues of the wild‐type and a strain of knockout mouse whose GPI‐DAF gene has been inactivated. By fluorescence‐activated cell sorting (FACS) analysis, we found that DAF protein is present on the wild‐type mouse erythrocytes and lymphocytes but no signal was detectable on the same cells of GPI‐DAF gene knockout mice. Both T and B lymphocytes and splenic macrophages express the GPI‐DAF gene but the expression level is higher on B lymphocytes than on T lymphocytes. Within the T cell population, both CD4⁺ and CD8⁺ T cells are positive. DAF protein was detected by immunohistochemistry at high levels on wild‐type mouse spermatids and mature sperm. In contrast, only mature sperm stained positive in the GPI‐DAF gene knockout mouse testis, suggesting that GPI‐DAF but not the TM‐DAF gene is expressed on spermatids. Examination of the fetoplacental unit at the day 7·5 stage revealed that GPI‐DAF but not the TM‐DAF gene is expressed in the maternal decidua cells surrounding the trophoectoderm of the embryo. No DAF expression was detected on trophoblast or the embryo proper. These findings suggest that although the TM‐DAF gene is irrelevant on mouse blood cells, the two DAF genes may have different roles in germ cell development and/or mature sperm function. Because complement receptor 1‐related gene/protein y (Crry) has been shown to be expressed on early mouse embryos, the complete lack of GPI‐DAF and TM‐DAF gene expression in early mouse development may explain the observed sensitivity of Crry‐deficient embryos to maternal complement attack.