Abstract: The subject of this research is the institution of witness protection, peculiarities of the formation of system of proof in investigation of crimes where possible threats can be present to the parties involved in a criminal procedure. The work discusses certain issues in the legal regulation of the state witness protection, as well as the peculiarities of decisionmaking on application of measures of state witness protection and its realization with consideration of present threats and the phases of progression of criminal activity. It is proposed that the complex multi-stage system of regulatory acts does not promote making substantiated decisions on state witness protection. Members of law enforcement ensuring protection of witnesses from various regions of the Russian Federation have been interviewed. The main conclusions consist in the proposals to introduce a number of changes into the current Criminal Procedure Code of the Russian Federation pertaining to proving the threats, their assessment and adequate legal solutions.