This study investigated the emissions of polychlorinated dibenzo-p-dioxins, dibenzofurans (PCDD/Fs) and polychlorinated biphenyls (PCBs) from 45-hr cold start-up operations (from the ambient temperature) of two municipal solid waste incinerators (MSWIs). Fifteen samples were collected during the whole process, while the sampling period was divided as follows: (1) the initial stage (25–250°C); (2) the second stage (250–850°C), and the final stage (850–1000°C). The peak of total (PCDD/F + PCB) (WHO2005-TEQ) concentration occurred during the second stage of the cold start-up. This could because the temperature in the combustion chamber reached 295–359°C, within the temperature window (250–450°C) of PCDD/F reformation by de novo synthesis. However, both PCDD/F and PCB (WHO2005-TEQ) concentrations were still 2.8–3.8 times higher than the regulated standards in Taiwan 45 hours after the cold start-up began, demonstrating significant memory effects. Higher PCB/(PCDD/F + PCB) TEQ fractions were observed during the initial stage of cold start-up. This is probably due to the higher volatilities of memorized PCB-126 and -169 than PCDD/F congeners, thus making them more easily released into the flue gas. On the other hand, the total (PCDD/F + PCB) emissions during 45-hr cold start-up were estimated at 46–68 mg WHO2005-TEQ.The annual (PCDD/F + PCB) emissions from normal conditions are generally estimated by the normal operating emissions factor without the cold start-up. The normal annual (PCDD/F + PCB) emission rates of the two MSWIs were 70.7–101 mg WHO2005-TEQ, including once cold start-up emission, and these increased to 142–480 mg WHO2005-TEQ, up by 65–458%, if one to eight times of cold start-up were included. Therefore, reducing unnecessary start-ups could be more important with regard to controlling the PCDD/F and PCB emissions than only attempting to increase the pollutant removal efficiency in the steady operations of MSWIs.