Lipopolysaccharide (LPS) from gram-negative bacteria activates B cells, enabling them to proliferate and differentiate into plasma cells. This response is critically dependent on the expression of TLR4, but other genes, such as RP105 and MHC class II, have also been shown to contribute to B cell LPS response. Here we have evaluated the role of genetic control of the B cell response to LPS at the single cell level by using limiting dilution analysis. This approach avoided the co-stimulatory and feeder-cell dependent effects that occur in bulk cultured B lymphocytes. We compared the response to LPS of peritoneal cavity (PEC) and splenic B cells on the BALB/c genetic background (LPS-low responder) to those on the C57BL/6J background (LPS-high responder) and their F1 progeny (B6xBc). Both PEC and splenic B cells from B6 exhibited 100% clonal growth in the presence of LPS, whereas BALB/c PEC and splenic B cells achieved only 50% and 23% clonal growth, respectively. Surprisingly, PEC B cells on the F1 (B6xBc) background behaved as high responders (close to 100 %, as in B6), while splenic B cells displayed a response that was closer to that of the low responder BALB/c strain (≈ 30 %), revealing a differential genetic control. Splenic follicular B cells on both the F1 and BALB/c backgrounds were also low responders, averaging 18 % and 25 % growth, respectively. Marginal zone B cells on the F1 and BALB/c backgrounds were moderately higher, achieving 45–50% growth. Adding CpG (the TLR9 ligand) to the LPS stimulus promoted pushed splenic B cell clonal growth in the low responder strain BALB/c up to 90%, showing that the non-response to LPS is a specific effect that cannot be attributed to a general deficiency of in vitro growth by the BALB/c cells. The data presented here reveals a previous unsuspected behavior in the genetic control of the B cell response to LPS, with an opposing impact in splenic versus peritoneal cavity B cells. These results suggest the existence of an as yet unidentified genetic factor exclusively expressed by coelomic B cells that contributes to the control the LPS signaling pathway in the B lymphocyte.