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A method is presented for modeling the nonstationary and correlated noise of the RF seeker for estimating the target acceleration and the relative kinematics for endo-atmospheric engagement. The estimator also incorporates the dynamics of the seeker track loop. The state model estimates the acceleration of the target directly along with relative position and velocity. This model also include the ratio of the air density and the ballistic coefficient and its time derivatives as elements of the state vector to account for the aerodynamic drag in the endo-atmospheric phase. Such formulations obviate the need for priori empirical models of air density and drag coefficient. Performance results of the proposed method have been compared with a well-known model from the literature with and without the model of the measurement dynamics and the nonstationary, correlated measurement noise under closed-loop guidance employing the augmented proportional navigation (APN) law for endo-atmospheric ballistic target tracking. It is clearly seen that the proposed method yields more accurate estimates of target acceleration and the relative kinematics.