The flow of two immiscible fluids was investigated in rectangular glass microchannels with equivalent diameters of 269 and 400$\mu m$. Deionised water, dyed toluene and hexane were selected as probe fluids. Flow patterns were obtained for Y- and T-junction of two micro-channels and monitored by a photo-camera. Volumetric velocities of water and organic phase varied between 1 and 6ml/h. The formation mechanism of slug and parallel flow was studied and the mass transfer performances of two flow patterns were compared. The shape of the interface between the immiscible liquids was controlled by a competition between the viscous forces and the local interfacial tension. The flow patterns could be correlated with the mean Capillary and Reynolds numbers. The mass transfer coefficients for parallel and slug flow were determined using instantaneous eutralisation (acid–base) reaction. The two flow patterns showed the same global volumetric mass transfer coefficients in the range of 0. 2–0. 5 ${s}^{-1}$, being affected mainly by the base concentration in water for parallel flow and by the linear velocity in the case of the slug flow.