Rapid prototyping is a fast and efficient way for the functional verification of Systems-on-a-Chip in an early stage of the design process. Because of the rising part of software in those systems the use and reuse of microcontroller IP cores is necessary to keep development cycles short. Today, prototyping of such IP cores is done with large and expensive hardware emulation machines consisting of many processor or FPGA-based prototyping boards. In this paper the authors describe an alternative prototyping method for microcontrollers using one low-cost FPGA-based prototyping board. The method is based on the efficient usage of all resources of the prototyping system to emulate special parts of the microcontroller.