In this contribution we present an automated microfluidic system that allows the full control of a hydrodynamically focused sample stream, both in position and width. The basis of the system is a microfluidic chip for hydrodynamic focusing. A dyed sample is optically detected by a CMOS camera mounted on a microscope. The optical setup yields a resolution of 0.5 mu m/pixel. By performing colour intensity analysis on acquired frames, the sample stream position and width are derived. With these parameters, the flowrates of programmable volume driven syringe pumps are actuated. The microfluidic system has been designed, validated, and successfully tested in time domain. Furthermore, the system design approach can be easily adapted for different microfluidic geometries. (C) 2011 Published by Elsevier Ltd.