In order to isolate the related genes in the development of systemic lupus erythematosus (SLE) in BXSB mice, bone marrow cells were seperated from the BXSB and C57-BL-6 mouse, poly(A) RNA was extracted, the cDNAs were synthesized by reverse transcription, and the differentially expressed genes were cloned by cDNA-representational difference analysis(RDA). Three novel genes were isolated, their accession numbers in GenBank are AF060113, AF060111, AF060110; at the same time, some genes that have been reported to be related to the development of SLE such as endogenous retrovirus and Line -1 reverse transcriptase were found. This can provide a novel method to do further research about autoimmune diseases.