The slip flow regime is very frequently encountered in fluidic microsystems working with gases. A significant research effort has been made by a number of groups for developing accurate models of flows in this regime. A series of different boundary conditions have been proposed in the literature; they require a careful comparison with experimental data for leading to a valuable discussion about their accuracy and their range of applicability. Unfortunately, the only available experimental data concern mass or volume flow rates, whereas the direct measurement of the velocity profile is necessary for separately analyzing the role of the boundary condition and the role of the accommodation coefficient. In this paper, we propose to develop a micro molecular tagging velocimetry (µMTV) setup for measuring the velocity profile in a rectangular microchannel in the slip flow and early transition regimes. The principle of the technique is presented and the technical choice of components for the setup is detailed. The main objective is to directly access the slip velocity at the wall.