Methods and systems are directed to creating a physical unclonable function (PUF) on a Field Programmable Gate Array (FPGA) and generating a unique signature for a device. The method includes, in part, designing a PUF by taking advantages of programmable logic elements on the FPGA, and extracting uninitialized values associated with one or more storage elements comprised in the PUF when the FPGA is powered up. The extracted uninitialized values can be combined to generate the unique signature for the device. The one or more storage elements can be bi-stable memory cells that are mapped to look up tables (LUTs) on the FPGA. The coordinates of these LUTs can be determined based on hamming distance analysis. Alternatively, the one or more storage elements can be memory cells associated with boundary scan cells of a boundary scan chain.