Subcompartments of the plasma membrane are believed to be critical for lymphocyte responses but few genetic tools exist to test their function. Here we describe a new X-linked B cell deficiency syndrome in mice caused by mutations in Atp11c, a member of the P4 ATPase family thought to serve as flippases concentrating aminophospholipids in the cytoplasmic leaflet of cell membranes. Defective ATP11c decreased the rate of phosphatidylserine translocation in pro-B cells, greatly reduced pre-B and B cell numbers independent of Bcl2-inhibited apoptosis or immunoglobulin gene rearrangement and abolished pre-B cell expansion in response to an Il7 transgene. The only other abnormalities noted were anemia, hyperbilirubinemia and hepatocellular carcinoma. These results identify an intimate connection between phospholipid transport and B lymphocyte function.