A method for programming of a plurality of programmable devices arranged in a JTAG boundary scan chain takes advantage of knowledge of a target system. The method speeds device programming and reduces system memory requirements. Raw data is extracted from high-level files. The raw data is stored in the target system. JTAG boundary scan chain information is coded into device programming software. Alternatively, the JTAG chain information is stored as data in the target system. The device programming software treats JTAG I/O registers of the programmable devices as concatenated shift registers. Data packets are assembled that include, for example, a byte of programming information, for each of the devices. The packets are shifted through into the JTAG chain. Bytes of the packet are aligned with, and loaded into, respective devices. Optionally, the validity of data loaded is checked by comparing it to the stored raw data. Invalid data is reprogrammed.