The present study has shown that cyanopropyl- (CN) bonded silica may be applicable for the fractionation by high pressure liquid chromatography (HPLC) of mass and mutagenic activity of organic extracts from some incinerator emissions. Dichloromethane-extractable organics from particles emitted by two different municipal waste incinerators and by a pilot-scale rotary kiln incinerator that was combusting polyethylene plastic were fractionated by HPLC, and the mutagenicity of the collected fractions was determined by means of a microsuspension mutagenicity assay with Salmonella TA98. The CN-bonded silica column provided high (80–100%) mass and mutagenicity recoveries for most emission extracts, and it fractionated the mutagenic activity. The results suggest that the emissions from municipal waste incinerators contain a high amount of direct-acting (-S9) mutagenic activity that is resolvable by HPLC using CN-bonded silica. Sub-fractionation of selected mutagenic HPLC fractions and subsequent analysis by gas chromatography-mass spectroscopy can be used to identify mutagenic species within complex incinerator emissions. The coupling of microsuspension bioassays to HPLC fractionation should be a useful tool for this type of analysis.