Emissions of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) from the stack flue gases of four medical waste incinerators (MWIs) and ten municipal solid waste incinerators (MSWIs) were investigated. The mean PCDD/F concentrations in the stack flue gases of these MWIs and MSWIs is 0.521 ng I-TEQ/Nm3 and 0.0533 ng I-TEQ/Nm3, respectively. In the stack flue gases of MWIs, OCDD, 1,2,3,4,6,7,8-HpCDD, 1,2,3,4,6,7,8-HpCDF and OCDF were the major congeners, while in MSWIs, OCDD and 1,2,3,4,6,7,8-HpCDD were the major ones. The mean PCDD/F emission factors (20.1 μg I-TEQ/ ton-waste) of the MWIs was about 210 times of magnitude higher than that of MSWIs, which was 0.0939 μg I-TEQ/ton-waste. In Taiwan, the annual emissions of PCDD/Fs from MWIs and MSWIs are 0.371 g I-TEQ/year and 0.737 g I-TEQ/year, respectively. Although the contribution of PCDD/Fs from MWIs to the atmosphere was 50.3% of that from MSWIs, it should be noted that most MWIs are equipped with a low stack and are situated in the proximity of the residential area and PCDD/F emissions from MWIs could significantly affect its surrounding environment.