This paper presents a detailed comparison of the kinetic analysis software packages SAAM II and PCNonlin/WinNonlin, based on benchmark modeling problems reported in "Pharmacokinetic andPharmacodynamic Data Analysis: Concepts and Applications" (Gabrielsson and Weiner, 1994) and seven additional models. For each model, both software packages were presented with identical implementations. Models were initially executed in PCNonlin or WinNonlin and automated comparisons with SAAM II made using Microsoft Test. Models investigated included one- and multicompartment models with nonlinearities, multiple inputs and samples, multiple simultaneous experiments, and linear equations. Maximum number of compartments, data sets, and parameters were 9, 5, and 10, respectively. We compared 88 different models, many of them in different configurations, e.g., different weighting schemes or different parameter limits. The total number of attempted comparisons between SAAM II and PCNonlin was 161, of which 142 executed without problems. Parameter estimates, their precision (standard errors), and model predictions were compared; a difference of 1% or less was considered "agreement". Observed differences, mainly in parameter standard errors, can be accounted for in terms of different optimization algorithms, convergence criteria, and individual capabilities. In general, there was good agreement (<1% difference) between SAAM II and PCNonlin in terms of parameter estimates and model predictions. However, due to differences in the optimization procedure, parameter standard errors showed considerable differences. Additionally, there were differences when multiple data sets were fitted, indicating the importance of different fitting procedures for interpreting multiple kinetic data sets. The full results of the comparison and the model files in SAAM II and PCNonlin/WinNonlin formats are available from the authors.