This study is carried out in a full-scale (1.25 t/h) medical waste incinerator (MWI), focusing on reduction characteristics of different air pollution control devices (APCDs) on trace pollutants [polychlorinated dibenzodioxins and dibenzofurans (PCDD/F)] and micropollutants (heavy metals) in flue gas. The APCD system effectively reduces the PCDD/F concentration to 5.32 ng/Nm(3) (0.07 ng I-TEQ/Nm(3) for toxic PCDD/F) with a removal efficiency of 87.95% (90.86% for toxic PCDD/F). The 2,3,4,7,8-PeCDF is the biggest contributor of toxic PCDD/F at each sampling site. The APCDs obviously influence the isomer distribution but do not change the dominant position of major isomers, and the proportion of PCDF is continuously decreased by different APCDs. The fabric filter coupled with active carbon injection (FF + ACI) removes 75.45% PCDD/F (94.81% for toxic PCDD/F) from flue gas and shows obviously higher removal efficiency on the PCDD/F congeners chlorinated in both 7 and 8 positions compared to other congeners. In addition, FF + ACI can also effectively remove most heavy metals from flue gas other than Hg. However, the memory effects of PCDD/F and Hg are observed at wet scrubbers in this study. Cr and As might have the potential to be indicators of PCDD/F according to their excellent correlation with PCDD/F concentrations. The results can benefit controlling the emissions of PCDD/F and heavy metals from MWI and give guidance to the other MWI plants.