Vancomycin is an antibiotic used for treating infections caused by bacteria which are resistant to other antibiotics, but in some of the treated patients it causes kidney damage. Since the currently known biomarkers of nephrotoxicity do not show sufficient sensitivity and specificity, it is necessary to find new biomarkers which would enable to discover disorders in kidney function in early stages and stop the therapy at the right time with the aim to prevent further development of kidney damage. The main goal of this study was to compare proteomic profiles of urine samples collected from patients on vancomycin therapy with and without clinical signs of kidney damage detected during the therapy in order to find potential protein biomarkers of vancomycin nephrotoxicity. Analysis of samples by one-dimensional gel electrophoresis showed that both quantity and composition of urinary proteins change depending on the day of therapy. Furthermore, significant differences in proteomic profiles of urine samples collected from patients with and without kidney damage caused by vancomycin therapy occur only after third, and are especially evident after seventh day of therapy, with the biggest differences observed within a range of molecular weights of about 25-75 kDa. Two-dimensional gel electrophoresis combined with MALDI-TOF/TOF revealed expression of keratin 1 type II, NGAL and retinol-binding protein 4 in urine of patient with kidney damage caused by vancomycin therapy, which suggests that those three proteins could present potential biomarkers of vancomycin nephrotoxicity. It is necessary to conduct further studies including larger number of patients in order to validate these results and to investigate their potential diagnostic and clinical significance.