Research groups in the field of functional electrical stimulation (FES) are often confronted with the fact that existing and commercially available FES stimulators do not provide sufficient flexibility and cannot be used to perform different FES tasks. The lack of flexibility of the commercial systems until now forced various FES research teams to develop their own stimulators. This paper presents a newly developed firmware and graphical programming software for the commercial Compex 2 stimulator which enhances the versatility and capabilities of the stimulator from a medical and therapeutic device to a neuroprosthesis and research tool. The new stimulator, called Compex Motion, can now be used to develop various custom-made neuroprostheses, neurological assessment devices, muscle exercise systems, and experimental setups for physiological studies. It can be programmed to generate any arbitrary stimulation sequence that can be controlled or regulated by various external sensors, sensory systems, or laboratory equipment. By interconnecting two or more Compex Motion stimulators, the number of stimulation channels can be increased to multiples of four channels, 8, 12, 16, 20, and so forth. The stimulation sequences and the control strategies are programmed and stored on exchangeable credit card-sized memory chip cards. The stimulator has four biphasic current-regulated stimulation channels and two general purpose analog input channels that can be configured to measure the output voltage of a variety of sensors such as goniometers, inclinometers, gyroscopes, or electromyographic (EMG) sensors. For real-time EMG control of the stimulation patterns, an EMG processing algorithm with software stimulation artifact blanking was implemented. The Compex Motion stimulator is manufactured by the Swiss company Compex SA and is currently undergoing clinical trials.