A study was conducted to observe the changes in polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F) levels and congener profiles in the flue gas of a hazardous waste incinerator during two start-up periods. Flue gas samplings were performed simultaneously through Air Pollution Control Devices (APCDs) (including boiler outlet, electrostatic precipitator (ESP) outlet, wet scrubbers (WS) outlet, and activated carbon (AC) filter outlet) in different combustion temperatures during a planned cold (long) start-up and an unplanned warm (short) start-up. The results showed that PCDD/F concentrations could be elevated during the start-up periods up to levels 3-4 times higher than those observed in the normal operation. Especially lower combustion temperatures in the short start-ups may cause high PCDD/F concentrations in the raw flue gas. Assessment of combustion temperatures and Furans/Dioxins values indicated that surface-catalyzed de novo synthesis was the dominant pathway in the formation of PCDD/Fs in the combustion units. PCDD/F removal efficiencies of Air Pollution Control Devices suggested that formation by de novo synthesis existed in ESP also when in operation, leading to increase of gaseous phase PCDD/Fs in ESP. Particle-bound PCDD/Fs were removed mainly by ESP and WS, while gaseous phase PCDD/Fs were removed by WS, and more efficiently by AC filter.