We have prepared 30W-class PEMFC stacks for portable powers and examined experimentally on the effect of gas diffusion layer (GDL) in water managing of the stack. Because miniature PEMFC stacks usually employ bipolar plates with small dimensions of flow field, they were strongly dependent on the thickness of GDL by affecting by-pass flow rate and water management ability of the stack. Hence, the stack performance was sensitively changed with clamping pressures of the stack by altering GDL thickness and in-plane gas permeability of the GDL containing in the stack. When we prepared the stack with high clamping forces it showed very stable performance behavior, while at low clamping pressures it revealed unstable behavior by poor water management and flooding of cells in the stack. In addition, the GDL thickness also affected the fuel utilization, particularly in case of reformed gas, for stable stack performance. Low clamping pressure required high amount of fuel gas compared to high clamping pressure for stable stack performance. It seems that the low clamping pressure of the stack causes high in-plane permeability of the GDL resulting in low pressure drop in the stack and cell flooding. These results strongly imply that the GDL thickness can be critical for the performance of the micro-stack by affecting the water management ability of the stack, particularly at high relative humidity conditions. Hence, the choice of optimum GDL and clamping pressure is very important for the high stack performance and stable operation of the stack.