Objective To investigate influence of genders on the activity of nuclear factor-kappa B (NF-κB) in lungs of endotoxemic rats. Methods Twenty female and 20 male Wistar rats were randomly divided into four groups as follow: female control group (n=10), male control group (n=10), male endotoxemic group (n=10), and female endotoxemic group (n=10). The endotoxemic rats model was made by injecting lipopolysaccharide (5 mg/kg) into the abdominal cavity. Tissue samples were collected from the lungs in different groups and electrophoresis mobility shift assay was used to measure the activity of NF-κB. The levels of serum TNF-α and estrogen were measured at the same time. Results There was no significant difference between the activities of NF-κB in male and female control groups (1.33±0.24 vs 1.47±0.40）, and there was also no significant difference between other items in these groups as well (Pgt;0.05). Yet, the activity of NF-κB (female: 12.10±2.89; male: 19.53±2.12) and the level of TNF-α 〔female: (4.10±0.72) ng/ml; male: (6.37±1.29) ng/ml〕 were significantly increased after injection of lipopolysaccharide (Plt;0.01), and the indices in female group were significantly lower than those in male group (Plt;0.01). Correlation analysis showed that there was a positive relation between the activity of NF-κB in lungs and the level of TNF-α (female: r=0.921 1, P=0.013; male: r=0.907 2, P=0.017), and there was a negative correlation between the activity of NF-κB and the level of estrogen (female: r=-0.887 5, P=0.017; male: r=0.872 3, P=0.022) in both male endotoxemic group and female endotoxemic group (Plt;0.05). Conclusion Gender may be one of the factors that influence the activity of NF-κB in the lungs of endotoxemic rats. While on the other hand, endogenous estrogen may protect the lungs of endotoxemic rats from injury by inhibiting the activity of NF-κB.