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Recent research has demonstrated the use of microfluidic devices and electro-kinetics in areas such as medicine, genetics, embryology, epidemiology and pollution analysis, where manipulation of particles suspended in liquid media is required. Micro-fabrication technology has made it possible to increase system complexity and functionality by allowing integration of different processing and analysis stages in a single chip. However, fully integrated and autonomous microfluidic systems supporting ad-hoc stimulation have yet to be developed. This paper presents a flexible, configurable and programmable stimulator for electro-kinetically driven microfluidic devices. The stimulator is a dedicated System-on-Chip (SoC) architecture that generates sine, triangle, and sawtooth signals within a frequency range of 1Hz to 20 MHz, capable of delivering single, dual, and superimposed waveforms, in a user defined test sequence for a selected time period. The system is designed to be integrated into complete, autonomous Lab-on-Chip, portable or implantable devices. As such, it is expected to help significantly advance current and future research on particle manipulation.