We report on the inclusion of a Ag/AgCl reference electrode on a microfluidic chip in a T-geometry. The position of this electrode, the position of the working electrode, the channel geometry, and fluid flow rates are explored in relation to interference and contamination at steady state. Experimental data, supported by computer simulations, suggests operation and design guidelines to avoid such contamination, thereby creating a reliable electrochemical flow cell. These results can be applied to any electrochemical, microfluidic cell with a geometry more advanced than a single parallel channel. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.007211jes] All rights reserved.