Hemodialysis (HD) is the most common therapy to treat end-stage renal disease (ESRD) patients. That is used to clear blood from metabolism end products and maintain water and electrolyte balance in patients’ body when failed kidneys unable to do that. Patient’s blood contact via dialysis filter (dialyzer) about 400 L of dialysis fluid that is mainly form of water and some electrolyte, this quantity of fluid contact can stimulate the production of pre-inflammatory markers due to carrying pathogens such as bacterial DNA fragments even in small quantity that can pass all filters to bloodstream stimulating production of IL-6. A total of 90 blood samples were collected from 45 patients under hemodialysis therapy in Baghdad Teaching Hospital, Gazy Alhariry general hospital, Al-khayal private hospital and Al-Muayad private hospital before and after 3 hours of HD therapy to detect IL-6 by ELISA technique. And from the same centers dialysis fluid and water samples were collected to detect bacterial DNA fragments. PCR technique using 16s universal bacterial primer showed presence of bacterial DNA fragments in dialysis fluid and water used to prepare it.The ELISA readings showed a variety in IL-6 levels higher in patients with low ultrafiltration UF rate than its level in patients with high UF and generally, the level of IL-6 in patients treated in centers with DF preparation direct water distribution system were lower than its level in patients treated in centers with indirect water distribution systems.