CD20 is a hallmark antigen of B lymphocytes. Its expression is restricted to precursor and mature B cells but it is not expressed on plasma cells. The protein is a membrane-embedded phosphoprotein that appears likely to transverse the membrane four times. Its function is unknown although CD20 has been variously proposed to play a role in B-cell activation, proliferation, and calcium transport. A unique homologue of human CD20 has been described in mouse, which also shows a B-cell-specific pattern of expression. Here we describe the generating of mice carrying a CD20 gene disruption. So far, we have failed to detect any major effect of the gene disruption on the differentiation and function of B lymphocytes as judged by the expression of surface markers, antigen receptor signaling, proliferative responses, or calcium uptake. We did note, however, that the mice homozygous for the gene disruption [generated by intercrossing (129 x C57BL/6)F1 CD20+/- heterozygotes] showed a substantial depletion of the sub-population of peritoneal B cells that lack expression of the B220 (RA3-6B2) isoform of CD45. The loss of the IgM+ 6B2- peritoneal B cells is not, however, attributable to the CD20 gene disruption itself. Rather, it segregates with a polymorphic difference between the 129 and C57BL/6 strains that is linked to the CD20 locus which, intriguingly, is itself close to the CD5 gene. This demonstrates that caution must be exercised when comparing the phenotypes of F2 litter-mates generated from crosses between 129 embryonic stem-cell-derived chimeras and mice of other strains.