This paper introduces a complete system-level design and integration of a portable direct methanol fuel cell (DMFC) system. We describe hardware and software design for the balance of plant (BOP) control, including a 32-bit microprocessor and electronics for actuators and sensors, focusing on reliable operation and protection of the DMFC system. Various BOP components are characterized to find the optimal design for better portability, reliability, and energy efficiency, and we suggest effective and robust design of control loops for them. We demonstrate a hybrid operation of the DMFC stack and Li-ion battery to maintain a constant stack output current regardless of the load current to maximize the performance. We emphasize the design of subsystems for power supply, measurement, actuator drive, and protection in detail. We verify the robust operation of BOP control against environmental changes such as orientation and pressure variations with an implemented control board. (C) 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.