Objective To study the influence of Apo E gene knockout on the lymphocytes. Methods Cells from the peripheral blood, spleen and bone marrow of Apo E knockout and wildtype mice were stained with kinds of antibodies, and analyzed by flow cytometry. Results Compared with wildtype mice, significant differences were found in B and T lymphoctes in the peripheral blood and spleen, but there was no significant difference in pre B cells, T lymphocytes in the thymus and long term hematopoietic stem cell in the Apo E knockout mice. Conclusion Numbers of B lymphocytes decreased in the peripheral blood and spleen, but there was no significant difference in B, T lymphocytes development, and numbers of long term hematopoietic stem cell in Apo E gene knockout mice.