An ElectroMagnetic analysis (EMA) technique is applied to Flash-based FPGA (Field Programmable Gate Arrays) ProASIC3E to measure the delay variability. Measurements show that delay variations can reach 40% according to the mapping, placement and routing used in the FPGA array, while the synthesis tool analysis show differences lower than 7%. Comparisons between the use of EMA technique in Flash and SRAM-based FPGAs are presented. The Flash-based FPGA configurable blocks and routing structures are modeled at the electrical level. Then, SPICE simulations are performed to compare the predictive variability to the measurements ones. Results obtained with EMA can support designers on selecting different parts of the FPGA array, such as distinct mapping, placements and routing wires according to application and provide a valuable feedback for the FPGA's manufacture company. © 2013 IEEE.