The paper presents a method to identify aerodynamic parameters from flight-test data, determine the uncertainty in the identified parameters, and estimate the model-form uncertainties in the aerodynamic model. This information is required for simulations designed to estimate the reliability of the system. An output error method is used in parameter estimation, and uncertainty in these estimates is based on the Cramér–Rao bounds. Validation data are then used to compare the values of the aerodynamic coefficients as predicted by the model to experimental data. These data are used to estimate the model-form uncertainty, which is represented as prediction intervals. These methods are used to analyze both synthetic and true flight-test data. The results validate the proposed method to estimate the aerodynamic parameters and the associated model-form uncertainties. The model-form uncertainties can be directly used to predict the uncertainty in the aircraft performance and probability of loss of control.