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We present an approach of how to perfect the skills of the students studying digital design related topics. Our teaching concept is problem-based and offers possibilities for “learning by doing”. We also provide special supplementary tools, which make teaching with a problem-based approach much easier. All tools are tailored to the learning process and are available for access or download from all over the world using the Internet. This permits to continue working on project assignments outside university. Students are given an interesting practical task and then are shown how to solve it using methodology and tools, which have been previously presented during course lectures. The FPGA-based development boards are both low-cost and powerful educational tools for prototyping and development of digital systems. Reprogrammability of FPGAs allows to implement and verify the full design itself, as well as to build early prototypes of the sub-circuits using the same development board.