Localization is the fundamental problem of intelligent vehicles. For a vehicle to autonomously operate, it first needs to locate itself in the environment. A lot of different odometries (visual, inertial, wheel encoders) have been introduced through the past few years for autonomous vehicle localization. However, such odometries suffers from drift due to their reliance on integration of sensor measurements. In this paper, the drift error in an odometry is modeled and a Drift Covariance Estimation (DCE) algorithm is introduced. The DCE algorithm estimates the covariance of an odometry using the readings of another on-board sensor which does not suffer from drift. To validate the proposed algorithm, several real-world experiments in different conditions as well as sequences from Oxford RobotCar Dataset and EU long-term driving dataset are used. The effect of the covariance estimation on three different fusion-based localization algorithms (EKF, UKF and EH-infinity) is studied in comparison with the use of constant covariance, which were calculated based on the true variance of the sensors being used. The obtained results show the efficacy of the estimation algorithm compared to constant covariances in terms of improving the accuracy of localization.