A security system for embedded systems, comprising: a PROTECTED SYSTEM comprising a CPU SYSTEM and a SECURITY DEVICE the CPU SYSTEM comprising one or more microprocessor cores for running CODE comprising machine-language instructions for controlling actions of the microprocessor cores of the CPU SYSTEM; the SECURITY DEVICE being an electronic integrated circuit separate from the CPU SYSTEM that is not and does not use any general purpose microprocessors, wherein the SECURITY DEVICE is irremovable from the PROTECTED SYSTEM; a PHYSICAL PRESENCE DEVICE being an electrical circuit connectable to the PROTECTED SYSTEM; and a PROGRAMMER being an electrical circuit or collection of circuits for generating CRYPTOGRAPHIC INFORMATION for storage on the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE the PROGRAMMER being connectable to the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE during construction of the PROTECTED SYSTEM and disconnectable during operation of the PROTECTED SYSTEM, and wherein the SECURITY DEVICE provides the only means of electrically connecting the PROTECTED SYSTEM to the PHYSICAL PRESENCE DEVICE or PROGRAMMER, the system further comprising the CRYPTOGRAPHIC INFORMATION received from the PROGRAMMER during construction of the PROTECTED SYSTEM and stored on the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE, wherein the CRYTPOGRAPHIC INFORMATION is unique to both the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE such that other PROTECTED SYSTEMS cannot share the same PHYSICAL PRESENCE DEVICE, and wherein when the PHYSICAL PRESENCE DEVICE is physically connected to the SECURITY DEVICE after construction and validated based on the CRYPTOGRAPHIC INFORMATION, electrical circuits within the PHYSICAL PRESENCE DEVICE enable one or more functions within the SECURITY DEVICE to: encrypt and load CODE or other data into protected storage; modify a state of the SECURITY DEVICE; or synchronize some of the CRYPTOGRAPHIC INFORMATION on either the PHYSICAL PRESENCE DEVICE or the SECURITY DEVICE. a PROTECTED SYSTEM comprising a CPU SYSTEM and a SECURITY DEVICE the CPU SYSTEM comprising one or more microprocessor cores for running CODE comprising machine-language instructions for controlling actions of the microprocessor cores of the CPU SYSTEM; the SECURITY DEVICE being an electronic integrated circuit separate from the CPU SYSTEM that is not and does not use any general purpose microprocessors, wherein the SECURITY DEVICE is irremovable from the PROTECTED SYSTEM; the CPU SYSTEM comprising one or more microprocessor cores for running CODE comprising machine-language instructions for controlling actions of the microprocessor cores of the CPU SYSTEM; the SECURITY DEVICE being an electronic integrated circuit separate from the CPU SYSTEM that is not and does not use any general purpose microprocessors, wherein the SECURITY DEVICE is irremovable from the PROTECTED SYSTEM; a PHYSICAL PRESENCE DEVICE being an electrical circuit connectable to the PROTECTED SYSTEM; and a PROGRAMMER being an electrical circuit or collection of circuits for generating CRYPTOGRAPHIC INFORMATION for storage on the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE the PROGRAMMER being connectable to the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE during construction of the PROTECTED SYSTEM and disconnectable during operation of the PROTECTED SYSTEM, and wherein the SECURITY DEVICE provides the only means of electrically connecting the PROTECTED SYSTEM to the PHYSICAL PRESENCE DEVICE or PROGRAMMER, the system further comprising the CRYPTOGRAPHIC INFORMATION received from the PROGRAMMER during construction of the PROTECTED SYSTEM and stored on the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE, wherein the CRYTPOGRAPHIC INFORMATION is unique to both the PHYSICAL PRESENCE DEVICE and the SECURITY DEVICE such that other PROTECTED SYSTEMS cannot share the same PHYSICAL PRESENCE DEVICE, and wherein when the PHYSICAL PRESENCE DEVICE is physically connected to the SECURITY DEVICE after construction and validated based on the CRYPTOGRAPHIC INFORMATION, electrical circuits within the PHYSICAL PRESENCE DEVICE enable one or more functions within the SECURITY DEVICE to: encrypt and load CODE or other data into protected storage; modify a state of the SECURITY DEVICE; or synchronize some of the CRYPTOGRAPHIC INFORMATION on either the PHYSICAL PRESENCE DEVICE or the SECURITY DEVICE. encrypt and load CODE or other data into protected storage; modify a state of the SECURITY DEVICE; or synchronize some of the CRYPTOGRAPHIC INFORMATION on either the PHYSICAL PRESENCE DEVICE or the SECURITY DEVICE.