Three-dimensional direct numerical simulations were performed for investigating the flow in a serpentine channel and the under-laying porous gas diffusion layer (GDL) of a micro polymer electrolyte fuel cell (PEFC). The flow field comprised three straight sections and two U-turns. The geometry was acquired with high-resolution (2.9 μm) in situ X-ray tomographic measurements on an operating cell. Simulations considered the GDL under dry and partially saturated conditions, whereby saturation was established via electrochemically produced water. A lattice Boltzmann (LB) methodology was adopted for simulating the single-phase (gas) transport in the actual 3D channel and porous GDL geometry. The global pressure drop in the dry GDL was dominated by the turns in the gas channel, while the pressure drops were quite small along the straight channel sections. In the wet GDL case, however, the pressure drop was mainly dictated by the neck-shaped passages created by the large water clusters inside the channel. Owing to the water blockage, the local accumulated cross-flows along the serpentine channel length, when normalized by the inlet channel flow, were substantially higher in the wet GDL, reaching local values up to 45% compared to 18% for the dry GDL. The implications are that in an electrochemically operating cell, the GDL under the rib would receive more gas (and thus O₂). The creation of cross-flows through the porous GDL would enhance cell performance under the ribs since diffusion will not be the main driving mechanism for oxygen transport and water evaporation. The analysis indicated that the flow field, although designed as serpentine, behaved like half-interdigitated (with a rib of 1.5 mm, half-serpentine flow field, depending on the state of channel flooding).