The development of microelectronic lab-on-a-chip devices (LOACs) can now be pursued thanks to advances in silicon technology. As these kinds of devices may integrate different functional units, much care has to be put in the design of control units which have to provide real-time control capabilities in order to deal with complex systems composed of sensors, actuators, signal conditioning and processing circuits. Moreover, reconfigurability and expandability are key design features to get a flexible and reusable architecture. The FPGA implementation of a control system for an existing LOAC is presented as a case study with emphasis on the advantages of a programmable device approach. The presented system has been implemented on an Altera EPF10K200S device and the achieved operating frequency is 20MHz. The device was successfully tested and experimental results are hereby shown.