The usage of cardiopulmonary bypass (CPB) in cardiothoracic surgery contributes to the activation of the inflammatory response. In certain cases, the systemic inflammatory response may be immoderate, leading to organ dysfunction, such as acute renal failure or multiorgan dysfunction. This study aimed to examine the effect of haemoadsorption (HA) therapy on inflammatory markers and renal damage indices during cardiopulmonary bypass and in the early postoperative period. We conducted a retrospective analysis of prospectively collected data in a single tertiary care center on patients operated between January 2021 and May 2022. The levels of inflammatory markers and renal parameters in blood samples (Interleukin (IL) 6, C-reactive protein (CRP), white blood cells, lactate, procalcitonin (PCT), and NT-proBNP, urea, creatinine, glomerular filtration rate (GFR), mechanical ventilation days and intensive care unit (ICU) days) were compared between the three groups. Data from the Jafron HA 330 (n = 20) and CytoSorb300 (n = 20) groups were compared with those from the control group (n = 20). All patients underwent cardiopulmonary bypass for more than 120 min. Baseline patient characteristics were similar in all three groups. Acute kidney injury (AKI) was diagnosed in 17 patients (28.3%); seven patients were in the Jafron HA 330, two in the CytoSorb300, and eight in the control group. We found that IL1α, IL 6, IL8, Lactate dehydrogenase, PCT, NT-proBNP, CRP, Leukocyte, and TNFα had no significant or clinical difference between the CytoSorb 300 and Jafron HA 330 adsorber groups. Our results indicate that haemoadsorption therapy does not significantly reduce the risk of AKI after prolonged CPB, but decreases the need for renal replacement therapy.