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An intercomparison has been set up to study the representation of the atmospheric chemistry of the pre-industrial troposphere in earth system and other global tropospheric chemistry-transport models. The intercomparison employed a constrained box model and utilised tropospheric trace gas composition data for the pre-industrial times at ninety mid-latitude surface locations. Incremental additions of four organic compounds: methane, ethane, acetone and propane, were used to perturb the constrained box model and generate responses in hydroxyl radicals and tropospheric ozone at each location and with each chemical mechanism. Although the responses agreed well across the chemical mechanisms from the selected earth system and other global tropospheric chemistry-transport models, there were differences in the detailed responses between the chemical mechanisms that could be tracked down by sensitivity analysis to differences in the representation of C1–C3 chemistry. Inter-mechanism ranges in NOx compensation points were about 0.17 ± 0.12 when expressed relative to the inter-mechanism average. Monte Carlo uncertainty analysis carried out with a single chemical mechanism put the intra-mechanism range a factor of three higher at 0.50 ± 0.12. Similar differences between inter-mechanism and intra-mechanism ranges were found for hydroxyl radical depletion but were up to a factor of six wider for ozone formation from incremental additions of organic compounds. The cause of the discrepancies between the inter- and intra-mechanism ranges was found to be the large uncertainties that are present in the laboratory determinations of the rate coefficients and product channel branching ratios of some key chemical reactions involving organic peroxy radicals and hydroperoxides. Whilst these large uncertainties are present in the laboratory determinations, there will be irreducible uncertainties in the predictions from the earth system and other chemistry-transport models of methane and tropospheric ozone trends since pre-industrial times and hence their contributions to the radiative forcing of climate change. Further definitive laboratory studies of the reaction rates and product yields of the reactions of the simple organic peroxy radicals and hydroperoxides are required to resolve and reduce current uncertainties in earth system and chemistry-transport model predictions.