I will study the flow of complex fluids (emulsions , wormlike micelles solutions) in microfluidic devices. The velocity profiles are measured using Particles Imaging Velocimetry. Shear banded flows are evidenced in wormlike micelles solutions. The role of the confining and of the nature of the boundaries conditions will be adressed. These experiments will be analysed in the framework of non local rheology. Experimental data dealing with concentrated emulsion will be presented. In this case, no shear banding is evidenced eventhough some dynamical heterogeneities are pointed out. The size of the heterogeneities is measured using confocal imaging.