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.The model used for EKF development was calibrated to transient engine data using a 2010 Cummins ISB engine with a production aftertreatment system consisting of a DOC, CPF and SCR. The EKF was then exercised for three different SCR outlets, sensor configurations: NOX only, NH₃ only and both NOX and NH₃. The EKF-estimated outlet NO, NO₂, and NH₃ concentrations were compared to measured experimental data using a mass spectrometer. Not surprisingly, the case where both NOX and NH₃ were measured at the SCR outlet and used as input to the EKF yielded the best results. The next best performance was achieved using only the NH₃ sensor. This was likely due to a better estimate of the NH₃ storage within the SCR and thus better estimates of the effect of the reactions. The results of the NOX sensor only case might be improved by using a better model of the NOX sensor.