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The effect that three extraction techniques (e.g., Soxhlet, ultrasound and microwave-assisted extraction) have on the toxicity, as measured by submitochondrial particle (SMP) and Microtox assays, of organic extracts was compared from three sources of airborne particulate matter (APM). The extraction technique influenced the toxicity response of APM extracts and it was dependent on the bioassay method, and APM sample source. APM extracts from microwave-assisted extraction (MAE) were similar or more toxic than the conventional extraction techniques of Soxhlet and ultrasound, thus, providing an alternate extraction method. The microwave extraction technique has the advantage of using less solvent volume, less extraction time, and the capacity to simultaneously extract twelve samples. The ordering of APM toxicity was generally urban dust > diesel dust > PM10 (particles with diameter < 10 microm), thus, reflecting different chemical composition of the samples. This study is the first to report the suitability of two standard in-vitro bioassays for the future toxicological characterization of APM collected from Puerto Rico, with the SMP generally showing better sensitivity to the well-known Microtox bioassay.