Micro-fuel cells are considered as promising electrochemical power sources in portable electronic devices. Performance of micro-fuel cells are closely related to many factors, such as processes of fabrication, designs of flow fields, and operating conditions. In the present research, micro-proton exchange membrane fuel cells (PEMFCs) and micro-direct methanol fuel cells (DMFCs) were systematically investigated from the aspects of structure design, bipolar/end plates (BPs) fabrication, and fuel cells evaluation. In chapter 3, compared with conventional machining and rapid prototyping (RP) technology, microelectromechanical system (MEMS) technology was the practicable method to fabricate the BPs with channels of a few microns width. Experimental and modeling methods were employed to analyze performance of the micro-PEMFC in chapter 4. Contact resistance changed significantly the distribution of overpotential in the micro-PEMFC and decreased the current output. Small dimensions of the micro-channel drastically affected the species transport and resulted in a non-uniform current distribution along channel direction at low cell potential (high current). In chapters 5, four kinds of flow fields, mixed multichannel serpentine with wide channels, single channel serpentine, double channel serpentine, and mixed multichannel serpentine with narrow channels, were applied to micro-PEMFCs. Results suggested that the micro-PEMFC with good performance should use the flow field with a mixed multichannel design and long micro-channels. In chapter 6, the same flow fields were studied in the micro-DMFCs. Concentration and flow rates of methanol solution affected performance of micro-DMFCs. A micro-DMFC with the long and narrow channels needed to take long time to reach the stable stage when an electric load on it was changed. In chapter 7, a passive air-breathing micro-DMFC with low loading of catalysts was developed. Performance of the passive micro-DMFC became poor with the increase in concentration of methanol solution. Power densities of the passive micro-DMFC drastically depended on the current scanning rate. Finally, cobalt phthalocyanine was introduced to platinum catalyst system to improve and optimize the micro-DMFCs. After heat-treatment at 635 oC, CoPc-Pt/C demonstrated good electrocatalytic activity for oxygen reduction reaction (ORR) and high methanol tolerance. However, CoPc-Pt/C heated at 980 oC showed a good electrocatalytic activity for MOR in DMFCs.