In the present work we investigated the effect of germanium (Ge) citrate, which has antioxidant properties, on functional and metabolic activity of neutrophils, degree of DNA damage and pathways of thymus and lymph node cell death under the conditions of systemic endotoxemia in mice. It was found that the administration of E. coli lipopolysaccharide (LPS) (3 mg/ kg) induced a systemic inflammatory process with significant damage to cells and organs. Introduction of LPS caused the activation of the nonspecific resistance cells (according to the nitroblue tetrazolium test and the lysosomal-cationic test), which is an important mechanism of the cytotoxic effect of LPS. There was severe damage to DNA of thymus and lymph node cells, reducing their viability and an increase in the number of cells with signs of apoptosis or necrosis. The use of Ge citrate under the conditions of LPS treatment reduced generation of reactive oxygen species in neutrophils, as evidenced by a decrease in the percentage of formazanpositive cells and the cytochemical index. The content of cationic proteins and inflammatory mediators, according to the average cytochemical coefficient, was also decreased. In addition, administration of Ge citrate resulted in a reduce of the degree of DNA damage in thymus and lymph node cells, as well as in weakening necrotic and apoptotic cell death. Thus, the use of Ge citrate had a protective effect on thymus and lymph node cells reducing their DNA damage and death, which can be mediated by the normalization of neutrophil functions revealed in our experiments. The data obtained indicate the promise of the use of Ge citrate in the complex prevention and treatment of endotoxin induced diseases in humans and animals.