Introduction: the article is focused on consideration of the nature of the Institute of pretrial agreement on cooperation in the Russian criminal proceedings. The author considers pre-trial cooperation agreement as one of the grounds for the application of state protection measures against the suspect and the accused. Materials and Methods: in the course of the research the materials of works on criminal procedure, provisions of Federal laws regulating the pre-trial cooperation agreement, as well as state protection of persons participating in criminal proceedings were used. In the process of scientific research were used analytical, comparative legal, logical, historical and system-structural methods. In addition, there was a synthesis of legislative practice on the topic of the study. Results: the conducted study allowed to made conclusion that the pre-trial agreement on cooperation in the legislation of the Russian Federation should be considered as one of the basis for the application of state protection with regard to the suspect or accused. Discussion and Conclusions: during the research the author comes to the conclusion that the Institute of the pre-trial cooperation agreement should be considered by the legislation of the Russian Federation as an independent basis for the application of state protection measures against the suspect and the accused. Since a person entering into a "deal with justice" automatically puts his / her life and health, as well as the life and health of relatives and close persons at risk.