The extended Kalman filter (EKF) and unscented Kalman filter (UKF) for nonlinear state estimation with both additive and nonadditive noise structures are presented and compared. Three different Global Positioning System (GPS)/inertial navigation system (INS) sensor fusion formulations for attitude estimation are used as case studies for the nonlinear state estimation problem. A diverse set of actual flight data collected from research unmanned aerial vehicles was used as empirical data for this study. Roll and pitch estimation results were compared with independent measurements from a mechanical vertical gyroscope to evaluate the performance. The performance of the EKF and UKF is compared in terms of noise assumptions, covariance matrix tuning, sampling rate, initialization error, GPS outages, robustness to inertial measurement unit bias and scale factors, and linearization. Similar sensitivity for this GPS/INS attitude estimation problem was found between the EKF and UKF for most cases. Small differences were seen between EKF and UKF for initialization error and GPS outages: the UKF was found to be more robust to inertial measurement unit calibration errors, and the EKF was determined to be more computationally efficient.