Recent studies in biomechanical modeling suggest a paradigm shift, in which the parameters of biomechanical models would no longer treated as fixed values but as random variables with, often unknown, distributions. In turn, novel and efficient numerical methods will be required to handle such complicated modeling problems. The main aim of this study was to introduce and verify genetic algorithm for analyzing uncertainty in biomechanical modeling. The idea of the method was to encode two adversarial models within one decision variable vector. These structures would then be concurrently optimized with the objective being the maximization of the difference between their outputs. The approach, albeit expensive numerically, offered a general formulation of the uncertainty analysis, which did not constrain the search space. The second aim of the study was to apply the proposed procedure to analyze the uncertainty of an ankle joint model with 43 parameters and flexible links. The bounds on geometrical and material parameters of the model were set to 0.50 mm and 5.00% respectively. The results obtained from the analysis were unexpected. The two obtained adversarial structures were almost visually indistinguishable and differed up to 38.52% in their angular displacements.