We have studied the effect of annealing on magnetotransport in Fe/Au multilayers grown on Si substrate by sputtering. The multilayer interface structure was studied by specular and off-specular x-ray reflectometry whereas macroscopic magnetic properties are studied using SQUID magnetometer. We observed a reduction in magnetoresistance on annealing film at low temperature of 100 and 1500C. Reduction in magnetoresistance is attributed to increase in interface roughness as observed in x-ray reflectivity measurements.