Resistance to tyrosine kinase inhibitors is an essential issue concerning targeted therapy in renal cancer. This research focuses on molecular background of resistance to axitinib and sorafenib observed from the very beginning of a standard two-dimensional cell culture in monolayer as well as in three-dimensional models (soft agar and suspension cultures). Resistance was observed only in commercially available human kidney cancer stem cells. Mass spectrometry analysis revealed several proteins which may be functionally connected with the resistance to axitinib in normoxia and to sorafenib in hypoxia.