The objective of this study was to examine the effects of feeding dairy cows with regular corn (RCS) or brown midrib (BMCS) corn silage on CH₄ and CO₂ emissions from manure storage. For this purpose, 8 lactating cows fed diets containing 59% of RCS or BMCS were used in a block design. Total manure (feces and urine) collection from each cow was performed on 2 consecutive days. Manure was mixed (1:1) with an inoculum from a bioreactor and stored (20°C) under anaerobic conditions in glass bottles (6 replicates/cow) for 17 weeks. Quantity of gas produced was measured daily and sampled to determine gas composition, while manure was sampled weekly to measure volatile fatty acid (VFA) and NH₃ concentrations. The MIXED procedure of SAS was used to determine the effects of corn silage cultivar on measured parameters and significance was declared at P ≤ 0.05. Cows fed BMCS-based diets excreted more (P < 0.01) manure (86 vs 64 kg/d, respectively) and organic matter (8.6 vs 6.5 kg/d, respectively) than cows fed RCS-based diets. Excretion of N averaged 370 g/d and was not affected (P = 0.16) by the dietary treatment. Compared with manure from cows fed RCS-based diets, manure from cows fed BMCS-based diets emitted more (P ≤ 0.01) CH₄ (173 vs 146 L/kg organic matter [OM]) and CO₂ (148 vs 118 L/ kg OM) during storage period. Total VFA concentration tended to higher (P = 0.08) in manure from cows fed BMCS compared with cows fed RCS, indicating more extensive degradation of OM during storage of manure when cows were fed BMCS vs. RCS. Losses of OM from manure of cows fed BMCS based-diets was higher (P < 0.01) than losses from cows fed RCS-based diets (38 vs. 31%). In conclusion, feeding BMCS-based diets to dairy cows can increase daily volatile solid excretion and CH₄ and CO₂ emissions (per kg volatile solids) compared with feeding RCS-based diets.