An eddy-permitting adjoint-based assimilation system has been implemented to estimate the state of the tropical Pacific Ocean. The system uses the Massachusetts Institute of Technology's general circulation model and its adjoint. The adjoint method is used to adjust the model to observations by controlling the initial temperature and salinity; temperature, salinity, and horizontal velocities at the open boundaries; and surface fluxes of momentum, heat, and freshwater. The model is constrained with most of the available data sets in the tropical Pacific, including Tropical Atmosphere and Ocean, ARGO, expendable bathythermograph, and satellite SST and sea surface height data, and climatologies. Results of hindcast experiments in 2000 suggest that the iterated adjoint-based descent is able to significantly improve the model consistency with the multivariate data sets, providing a dynamically consistent realization of the tropical Pacific circulation that generally matches the observations to within specified errors. The estimated model state is evaluated both by comparisons with observations and by checking the controls, the momentum balances, and the representation of small-scale features that were not well sampled by the observations used in the assimilation. As part of these checks, the estimated controls are smoothed and applied in independent model runs to check that small changes in the controls do not greatly change the model hindcast. This is a simple ensemble-based uncertainty analysis. In addition, the original and smoothed controls are applied to a version of the model with doubled horizontal resolution resulting in a broadly similar “downscaled” hindcast, showing that the adjustments are not tuned to a single configuration (meaning resolution, topography, and parameter settings). The time-evolving model state and the adjusted controls should be useful for analysis or to supply the forcing, initial, and boundary conditions for runs of other models.