The article discusses legal basis for organizing the activities of the Ombudsman (Commissioner for Human Rights in Russian Federation) with the penitentiary system in the field of ensuring human rights, makes a structural analysis of the subject of incoming appeals to the Commissioner for Human Rights in Russian Federation, and also highlights the main areas of interaction in the field of ensuring human rights. In connection with the humanization of criminal and criminal-executive policy of Russia, the number of convicts has significantly decreased, material and household and medical support has improved, etc. As of August 1, 2020, 496 791 people were kept in the institutions of penitentiary system. (minus 27,137 people compared to 01.01.2020). At the same time, some problems regarding the protection of rights of suspects, accused, and convicted persons in the penal system continue to exist. The search for ways to improve penal system, its social reorientation and humanization determine the appeal to a new type of control over the observance of rights and legitimate interests of both convicts and employees of Federal Penitentiary Service of Russia - the institution of Ombudsman in Russian Federation, since problems related to observance of human rights in this area can accumulate for a long time, however, negative consequences of their non-resolution will further affect society and the state as a whole. The interaction of the Commissioner for Human Rights in Russian Federation and the penal system is manifested primarily in the field of ensuring human rights.