The present invention provides an efficient programming verification system for Programmable Logic Devices (PLDs). Based upon IEEE JTAG standard boundary scan test architecture, the invention provides a novel test architecture including a configuration register and a signature analyzer coupled between the TDI and TDO pins of the JTAG architecture. The configuration register of the invention comprises three parts: an address register/counter, a data register, a status register. The address register/counter performs dual functions depending upon an instruction received by an instruction register. The invention eliminates the need to load each address sequentially into the address register/counter for programming by enabling the address register/counter to auto-increment the address for memory locations. After loading an initial address value, the address register/counter automatically increments the address for programming memory cells. To verify PLD programming, the invention applies a signature analyzer coupled between the TDI and TDO pins. A single input linear feedback shift register (SISR) or multiple LFSR (MISR) can be used to implement a signature analyzer in accordance with the invention. SISR or MISR uses a characteristic polynomial to generate a near-unique signature checksum for an input sequence. The accumulated signature checksum is then provided serially through the TDO pin for inspection.