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Chemical sensitivity analysis (CSA) is a new probing tool for sampling sensitivities to chemistry parameters during a three-dimensional (3-D) simulation. CSA was applied to rank all of the parameters in the Carbon Bond 6 revision 4 (CB6r4) mechanism and to create an ensemble of six chemical mechanisms representing higher and lower O3formations than CB6r4. This ensemble of mechanisms was used to estimate the uncertainty from the chemistry in a 3-D simulation and combined with uncertainties from other model inputs obtained from calculations of their sensitivities. The overall uncertainty (1σ) in O3predictions for eastern Texas was 10–11 ppb in the Gulf of Mexico near Galveston and 7–8 ppb in much of the rest of the domain on the higher O3days of June 2012. As a percent of the O3concentration, the uncertainty was more uniform over the domain, 11–14%. Chemistry and emissions make the largest contributions to the O3uncertainty. Uncertainty in the dry deposition velocities is less important in urban areas and the Gulf, but it is similar in importance to the uncertainty in chemistry and emissions at most other locations. Uncertainty in O3boundary concentrations is the least important.