This study presents the comparison of three protein extraction methods in the investigations of clear cell Renal Cell Carcinoma tissue. For protein isolation, we applied: phenol extraction according to Hurkman and Tanaka (1986) protocol (method 1), whole tissue lysis in urea-containing buffer (method 2) and commercially available protein isolation kit (2-D Clean-up Kit) (method 3). Statistical analysis indicated that the additional preparation steps including extraction and purification of proteins by 2-D Clean-up Kit significantly increased the quality of obtained data. We believe that gathered information could be a valuable lead for researchers involved in proteomic studies of renal tissue.