The invention is directed to a treatment of diseases that are accompanied by quantitative and/or qualitative changes of blood extracellular DNA and, more particularly, to a treatment of systemic bacterial, fungal and protozoan infections. The inventive method comprises introducing a treatment agent into a circulating blood system of a patient diagnosed with systemic infection caused by bacteria, fungi or protozoa, wherein said treatment agent destroys extracellular DNA in said blood of said patient and wherein said treatment agent used to destroy said extracellular DNA is a DNase enzyme: said agent being administered in doses and regimens which are sufficient to decrease the average molecular weight of circulating extracellular blood DNA in the blood of said patient； such decrease in the average molecular weight can be measured by gel electrophoresis of extracellular blood DNA fraction from the blood of said patient. A DNase enzyme may be applied in a dose and regimen that provide a DNase DNA hydrolytic activity measured in blood plasma that exceeds 1.5 Kunitz units per 1 ml of blood plasma for more than 12 hours within a period of 24 hours.
