As supply of natural gas (NG) is limited, more attention is being given to operating fuel cells on syngas derived from gasification of feedstocks such as coal and biomass. Ammonia (NH 3 ) is one of the problematic contaminants contained in syngas produced from these nitrogen containing feedstocks. NH 3 can be easily oxidized to nitric oxide (NO) in a combustion process and thus if present in the anode exhaust gas would be problematic.The potential effects of NH 3 (particularly at low levels) on fuel cell system performance have not been well studied. The former studies on NH 3 have been limited to either the reforming process alone or testing the fuel cell at the cell level with NH 3 containing gases. No studies have been accomplished on a fuel cell system level basis. Objectives of this work are to obtain a comprehensive understanding of fuel cell system performance on syngas containing NH 3 using an integrated SOFC reformer system. Detailed analysis is conducted within the three major reacting components -indirect internal reformer, SOFC stack and combustion zone. Various simulation tools (etc., CHEMKIN, ASPEN, APSAT) are utilized for analysis. Results show that NH 3 conversion (into N 2 and H 2 ) in the internal reformer is about 50% when temperature is 750°C. NH 3 conversion (into N 2 and H 2 ) in the SOFC stack can affect NO x emissions significantly. More than 50% NH 3 left from SOFC stack can convert into NO x in the combustion zone. Experimental study is also planned to validate the theoretical results.