A box model using measurements from the Mexico City Metropolitan Area study in the spring of 2003 (MCMA-2003) is presented to study RO<sub>x</sub> (RO<sub>x</sub>=OH+HO<sub>2</sub>+RO<sub>2</sub>+RO) radical cycling in the troposphere. Model simulations were performed with the Master Chemical Mechanism (MCMv3.1) constrained with 10 min averaged measurements of major radical sources (i.e., HCHO, HONO, O<sub>3</sub>, CHOCHO, etc.), radical sink precursors (i.e., NO, NO<sub>2</sub>, SO<sub>2</sub>, CO, and 102 volatile organic compounds VOC), meteorological parameters (temperature, pressure, water vapor concentration, dilution), and photolysis frequencies. <br></br> Modeled HO<sub>x</sub> concentrations compare favorably with measured concentrations for most of the day; however, the model under-predicts the concentrations of radicals in the early morning. This "missing reactivity" is highest during peak photochemical activity, and is least visible in a direct comparison of HO<sub>x</sub> radical concentrations. The true uncertainty due to "missing reactivity" is apparent in parameters like chain length, and ozone production (P(O<sub>3</sub>)). For example, the integral amount of ozone produced could be under-predicted by a factor of two. Our analysis highlights that apart from uncertainties in emissions, and meteorology, there is an additional major chemical uncertainty in current models.