The three-dimensional flow structure of a bubble-train flow in a square capillary of 2 mm width is investigated numerically. Using the volume of fluid method for tracking the phase-interface direct numerical simulations in a cubic flow unit cell are performed for a void fraction ε=33% and two different values of the capillary number ( Ca B=0.205 and 0.043). Comparison of computed global flow parameters with available experimental data shows good agreement. Though for both capillary numbers the bubble is fully axisymmetric, quite different flow structures in the bubble and in the liquid slug are observed. This suggests that the flow conditions in miniaturized devices for chemical processing involving two-phase flow in square or rectangular mini- or micro-channels are very sensitive, indicating a certain potential for careful optimization.