More than likely your Honda Civic does not have an EGR valve. Our Emissions Application Guide indicates 2000 year model Honda engine 1.5 and 1.6 liter are not equipped with EGR valves. Vehicles without EGR valves have a tendency to develop CAT problems sooner then those which are equipped. Due to the fact there is no EGR valve to reduce NOx, this operation is performed by the CAT, and proper fuel management.
If after fuel and ignition systems are inspected and either no faults found or faults found and repaired, yet your Honda still fails the smog test, consideration should be given to a defective CAT.
