This study was designed to investigate the biocompatibility of hemodialysis procedures, largely depending on the contact of patient's blood with the dialysis membranes. We addressed the issue by comparing the content of the proteolytic enzymes collagenase and cathepsin B and that of neutrophil myeloperoxidase (MPO) and C-reactive protein (CRP) in the blood before and after a single session treatment and a full course of successive 8-week-long therapies with three types of hemodialysis: low-flux (lfHD), high-flux (hfHD), and post-dilution hemodiafiltration (HDF). The study included 19 patients with chronic nephropathy. We found that collagenase significantly increased after a single session of each type of hemodialysis. Cathepsin B tended to decrease after single sessions; the decrease reached significance only after hfHD. CRP increased significantly after single hfHD and HDF treatments. These changes were meager, with no differences depending on the dialysis type, and their significance was lost after 8-week-long therapy, except the persisting increase in CRP after HDF. Neutrophil MPO apparently was not activated during any type of dialysis, as its content was below the detection threshold. We conclude that all three types of hemodialysis are compatible with the biological system, so that they would rather unlikely lead to clinically harmful effects in chronically hemodialyzed patients. Nonetheless, proteolytic enzymes and myeloperoxidase seem hardly appropriable estimators of hemodialysis biocompatibility due to meager and variable changes. Upregulation of C-reactive protein, on the other hand, expresses a general pro-inflammatory propensity of hemodialysis and is not a suitable estimator of biocompatibility either.