The molecular origin of X-linked hyper IgM syndrome has recently been identified as a defect in the ligand of CD40, gp39, a protein expressed on the surface of activated T cells. The availability of detailed pedigrees for three families with affected males allowed assessment of the random or nonrandom nature of the inactivation of the defective X chromosome as well as a determination of the origin of the mutation. X chromosome inactivation was studied because of the relevance to the ability to detect carriers of HIGM1 and the potential for phenotypic effect in the carriers. Using immunostaining, PCR, and DNA sequencing, we found that the defective gene for gp39 is not selectively inactivated. Even in the presence of extremely skewed inactivation, normal levels of serum Ig were found. In carriers in which the defective gene is predominantly expressed, staining alone revealed the carrier status reliably while cloning and sequencing of the cDNA was necessary when the normal gene was predominantly expressed. Unlike some other X-linked defects where extreme Lyonization may lead to disease, a small population of cells expressing the wild-type gp39 is sufficient to maintain normal humoral immunity and prevent the clinical symptoms of X-HIM.