This study investigates the polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/F) profiles of output materials and the influence of Cl content of input materials during the incineration of laboratory waste. The specimens, namely bottom ash (BTA), first quenching tower ash (FQA), secondary quenching tower ash (SQA), baghouse ash (BHA), and stack flue gas (SFG), were sampled and analyzed using high-resolution gas chromatography/high-resolution mass spectrometry, field-emission scanning electron microscopy (FE-SEM), ion chromatography, and X-ray diffraction (XRD). The Cl content was highest in FQA, followed by that in SQA, BHA, and BTA, and most of the Cl existed in soluble form, especially for FQA and SQA. The Cl mass was mainly distributed in FQA and BTA during incineration. The PCDD/F content of ash in each category was highly related to the Cl level in the input materials. The PCDD/Fs of all ashes and the particulate phase of SFG were mainly 7-Cl or 8-Cl PCDD/Fs, but those of the gas phase in SFG were mainly 4-6 Cl PCDD/Fs. In addition, an increase of Cl in the input materials increased the fractions of 7-Cl and 8-Cl PCDD/Fs. The XRD analysis results indicate that the main crystalline phase in fly ashes was NaCl. FE-SEM images show a porous granular morphology, which is consistent with the XRD analysis results.