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Engine and flow reactor experiments were conducted to determine the impact of biodiesel relative to ultra-low-sulfur diesel (ULSD) on inhibition of the selective catalytic reduction (SCR) reaction over an Fe-zeolite catalyst. Fe-zeolite SCR catalysts have the ability to adsorb and store unburned hydrocarbons (HC) at temperatures below 300°C. These stored HCs inhibit or block NOx-ammonia reaction sites at low temperatures. Although biodiesel is not a hydrocarbon, similar effects are anticipated for unburned biodiesel and its organic combustion products. Flow reactor experiments indicate that in the absence of exposure to HC or B100, NOx conversion begins at between 100° and 200°C. When exposure to unburned fuel occurs at higher temperatures (250°-400°C), the catalyst is able to adsorb a greater mass of biodiesel than of ULSD. Experiments show that when the catalyst is masked with ULSD, NOx conversion is inhibited until it is heated to 400°C.