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This paper focuses on the development of an Extended Kalman Filter for estimating internal species concentration and storage states of an SCR using NOX and NH₃ sensors. The motivation for this work was twofold. First, knowledge of internal states may be useful for onboard diagnostic strategy development. In particular, significant errors between the outlet NOX or NH₃ sensors, reconstructed from estimated states, and the measured NOX or NH₃ concentrations may aid OBD strategies that attempt to identify particular system failure modes. Second, the EKF described estimates not only stored ammonia but also NO, NO₂ and NH₃ gas concentrations within and exiting the SCR. Exploiting knowledge of the individual species concentrations, instead of lumping them together as NOX, can yield improved closed loop urea controller performance in terms of reduced urea consumption and better NOX conversion.