Using an Unscented Kalman Filter (UKF) as the nonlinear estimator within a Global Positioning System/Inertial Navigation System (GPS/INS) sensor fusion algorithm for attitude estimation, various methods of calculating the matrix square root were discussed and compared. Specifically, the diagonalization method, Schur method, Cholesky method, and five different iterative methods were compared. Additionally, a different method of handling the matrix square root requirement, the square-root UKF (SR-UKF), was evaluated. The different matrix square root calculations were compared based on computational requirements and the sensor fusion attitude estimation performance, which was evaluated using flight data from an Unmanned Aerial Vehicle (UAV). The roll and pitch angle estimates were compared with independently measured values from a high quality mechanical vertical gyroscope. This manuscript represents the first comprehensive analysis of the matrix square root calculations in the context of UKF. From this analysis, it was determined that the best overall matrix square root calculation for UKF applications in terms of performance and execution time is the Cholesky method.