An estimation strategy is presented for determining inlet and outlet composition of catalytic partial oxidation (CPDX) of methane over rhodium catalyst using simple, fast measurements: temperature, and thermal conductivity. A 1-D high fidelity simulation model for CPDX studied in Ref. [1] for a portable fuel cell application is developed and enhanced for transient experiments. Process dynamics are analysed to demonstrate how solid temperatures along the axes of the reactor reflect the endothermic/exothermic interplay of reactions during a process upset. Model reduction is then used to obtain a low complexity model suitable for use in a moving horizon estimator with update rates faster than 0.02 s. System theoretic observability analysis is then conducted to predict the suitability of different measurement designs and the best locations for temperature measurements for estimating both inlet and outlet gas mole fractions for all species. Finally, a Moving Horizon estimator is implemented and simulation experiments are conducted to verify the accuracy of the estimator. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.