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Microcontrolled systems coupled biosensors have attracted attention. Here, we describe an automated and portable microcontrolled pumping flow system (μC-PFS) developed to biosensing application. The flow system is fully automatic, portable, it works in battery module and it dispenses the use of microcomputer and the manual operations. This device presents mainly a microcontroller as central processing unit (CPU), an aquarium air pump and three-way solenoid valves to propulsion and the volume control of aliquots inserted in the flow system.