Abstract An a priori prediction of multiphase flow pattern in micro-capillaries or microstructured reactors (MSR) is required for their rational design. The state-of-the-art numerical models require huge computational efforts. In the present work, an analytical model based on flow stability analysis has been applied to study the flow patterns in MSR. In order to simplify the task, a coaxial capillary geometry was chosen as a model of MSR and the two-phase flow was characterized in terms of the rate of perturbation in relation to the axial velocity. Liquid–liquid flow experiments were carried out in glass micro-capillary equipped with high-speed camera under various operating conditions such as flow velocity, flow ratios and viscosity ratios. The volume of fluid (VOF) model by ANSYS Fluent software was applied to predict the flow pattern details numerically. The results obtained were consistent with the experimental observations. Finally, the experimental and simulation results were rationalized in terms of dimensionless numbers allowing simple a priori prediction of the flow pattern in MSR.