Previous algorithms in the term of designing mostly focused on separate sections of fuel cells. They addressed purpose of optimization, which only includes individual specific terms of fuel cells (such as membrane, electrodes, channels, electrolyte,...). New comprehensive algorithm presented in present study is based on global optimization and macro-model development which covers all detail correlations with boundary limitations. The exergy-cost model is an additional tool for results evaluation which may lead to shifting optimum results. The approach steps are: center dot identification, categorization and formulating of irreversibilities cause voltage drops; center dot founding optimum operational working point, based on power and efficiencies maximization; center dot sensitivity analysis and quantification for potential drop effects in proposed macro-model; center dot optimum engineering design for two case studies of 97 kW and 60 W; center dot comparison of the model results with experimental data as well as previous literature test running results by HPR and efficiency targets; center dot re-evaluating the results with exergy-cost model for design optimization. (c) 2006 Elsevier B.V. All rights reserved.