Atmospheric chemical mechanisms describe the photolysis and oxidation reactions of volatile organic compounds (VOCs), including bimolecular and unimolecular reactions of product radicals. Fully explicit representation of a single VOC can require thousands to millions of chemical reactions and species. Consequently, explicit chemical mechanism generation has proceeded through the use of automated tools that rely on observational data and structure activity relationships (SARs) to estimate rate coefficients and branching ratios. Here we compare, for the first time, two automated mechanism generators, GECKO-A (Generator of Explicit Chemical Kinetics of Organics in the Atmosphere and SAPRC MechGen (SAPRC Mechanism Generator). We specifically compare mechanisms for ten representative VOCs and the resultant properties of generated product mixtures as relevant for atmospheric chemistry. The observed differences in product mixtures can be explained by systematic differences between the mechanism generators after the initial reaction steps. GECKO-A has a more detailed representation of photolysis, including Norrish type-2 photolysis, which results in the formation of reactive alkenes from aldehydes. MechGen includes more alkoxy radical isomerization processes and autoxidation via H-shift reactions, the latter of which are not currently included in GECKO-A. Also MechGen assumes fast cyclization of alkyl radicals to form lactones or carbonates, which is not assumed by GECKO-A, and for which available theoretical predictions are inconsistent. These differences highlight needs for additional experimental data, particularly for uncertain products and yields, as well as for near continuous updating of these mechanism generation tools as sufficient data and new SARs become available.