The failed attempt to express HIV-gp41 in E. coli led to the investigation of HIV-gp41 segments, which is responsible for the toxicity to E. coli cells. A series of deletion mutants containing different regions of gp41 gene were constructed and expressed in E. coli BL21(DE3) strain. After IPTG induction, the high mortality of host bacteria was observed in host bacteria carrying the deletion mutants of gp41 gene except for those transformed with pET-HN2; coordinately, the mRNA transcripts of the gp41 was rapidly decreased; and the release of [3H]uridine increased upon induction. All these data suggested that GP41 protein has a cytotoxic effect on E. coli, and it is the cytotoxicity of the gp41 gene product that contributes to the high mortality when expressed in E. coli.