In the article the materials of individual studies of the main security problems in microcontrollers operating as part of control systems of both general and specialized devices were considered and analyzed. In particular, the main trends of security threats were analyzed and the main attacks vectors were presented. Foreign and domestic experience of manifestation of unauthorized influences and cyber threats in the main most critical places of microcontroller architecture is analyzed. The analysis showed that the basic places of security threats and interventions to the microcontroller are: registers, stack, LPA, memory (EEPROM and Flash), input-output ports, circuits and interfaces for data transfer to the MC, circuits for additional functionality for connecting to external peripheral devices and channels for connecting the clock oscillator. In addition, explorations were carried out on the main threats of the microcontroller system memory, namely: interference with direct memory access, access to control registers and access to the microcontroller buffer, buffer stack overflow, remote code execution, external access and attacks on secondary channels (including via external data lines in the MC), changing the order of addressing in the MC, changing / replacing the values of addresses and stack numbering, interfering with the work of data registers and indicating the state of the input / output ports of the microcontroller. A number of protection mechanisms for microcontrollers have also been studied, which together can reduce the risks of unauthorized actions on the microcontroller system. These include: cyclic code redundancy control, power monitoring and resource monitoring, the using of isolation and control of the functionality of the clock system, control of the integrity and reliability of the memory contents, control of external physical and electrical parameters of the microcontroller, virtualization of the main computing process and its multi-level redundancy and restoration of previous states, the using of cryptographic systems and data processing algorithms, the using of multi-level software and hardware isolation.