Logic emulators are extensively used for research and educational purpose in the field of digital systems design. Development of programmable devices enabled hardware emulation of complex digital circuits and systems. Comparing to the traditional digital model simulation, the physical implementation of the circuit on the emulator platform enables real application research. There are a lot of commercial programmable development boards available from the vendors of the FPGA devices. They are typically equipped with plenty of peripheral units and designed as stand-alone boards. On the other hand, a custom system can be specifically designed for prototyping and verification requirements of the user, e.g. verification of IP cores for a specific bus. This paper presents a custom programmable logic emulator developed in our laboratory and the design tools used in digital circuits education. The architecture of the emulator is based on two programmable devices with a PC interface. We will present some educational applications of the logic emulator. Students begin with learning the basic digital design principles using traditional tools and a novel micro-operation based design entry method. They are encouraged to study all the details of the programmable board and the design software. Later they are able to implement required course or diploma projects and master the whole design process.