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This research investigated the harvest, ambient pre-treatment, and storage of whole-plant corn as an alternative to conventional systems where corn grain and stover are fractionated at harvest. Harvesting the whole-plant, both grain and most of the above ground stover, after physiological maturity can reduce the intense logistics challenges typically associated with corn harvest and expand the harvest window. To determine the feasibility of the proposed system, corn was harvested at 65 to 16% whole-plant moisture (w.b.) using a forage harvester and then ensiled in pilot scale silos. Ambient pretreatment during storage was investigated using both dilute acid and lime. Both pretreated and control whole-plant silages were well conserved during anaerobic storage with dry matter (DM) losses generally less than 4%. Hydrodynamic separation of the grain and stover fractions after storage was found to be more effective at fractionating starch and fiber than conventional dry grain harvest, and both fractions had desirable composition. Pretreatment at storage with sulfuric acid significantly enhanced stover cell wall enzymatic degradability and subsequent fermentation to ethanol, increasing the cellulose conversion efficiency by 19, 11, and 4 percentage units for sulfuric acid pretreatments of 100, 30, and 10 g(kg DM)-1, respectively. The whole-plant harvest and storage system shows promise as a viable alternative to conventional corn grain and stover systems for producing feedstocks for biochemical conversion.