In this paper new magnetron sputtering system for multilayers deposition has been presented. The system allows sputtering of different materials from 4 targets in low pressure of working and reactive gas (oxygen, argon, oxygen + argon). Manufactured structures can be build from films, which have gradient concentration of dopant.Also the doping process can be performed with high precision in continuous or in pulse way. The high doping precision and possibility of deposition of multilayers without interruption of the sputtering process was received after application of a special designed magnetron pulse supplies.Thanks of that the system allows on manufacturing of the multilayers, which connect properties of different single films (dielectric, semiconducting and conducting) in one structure.