This paper discusses the design of a FPGA-based Bit Error Ratio (BER) measurement system in a serial communication link under electromagnetic emissions. The BER measurement is an important figure for the reliability of digital communication systems. Generally, the equipment involved to measure BER is prohibitively expensive. This paper demonstrates the design, construction and verification of an Open Source System (OSS), with all design files being made freely accessible to the public for use in general or highly specialized BER measurements. The methods used for programming the Hardware Description Language (HDL) modules were done as simple as possible to facilitate easy integration into experiments for academics with limited experience in HDL usage.