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Electronic cigarette (e-cigarette) market increased by 122% during 2014–2020 and is expected to continue growing rapidly. Despite their popularity, e-cigarettes are known to emit dangerous levels of toxic compounds (e.g., carbonyls), but a lack of accurate and efficient testing methods is hindering the characterization of e-cigarette aerosols emitted by a wide variety of e-cigarette devices, e-liquids, and use patterns. The aim of this study is to fill this gap by developing an automated E-cigarette Aerosol Collection and Extraction System (E-ACES) consisting of a vaping machine and a collection/extraction system. The puffing system was designed to mimic e-cigarette use patterns (i.e., power output and puff topography) by means of a variable power-supply and a flow control system. The sampling system collects e-cigarette aerosols using a combination of glass wool and a continuously wetted denuder. After the collection stage, the system is automatically washed with absorbing and extracting liquids (e.g., methanol, an acetaldehyde-DNPH solution). The entire system is controlled by a computer. E-ACES performance was evaluated against conventional methods during measurements of nicotine and carbonyl emissions from a tank type e-cigarette. Nicotine levels measured using glass fiber filters and E-ACES were not significantly different: 201.2 ± 6.2 and 212.5 ± 17 μg/puff ( p = 0.377), respectively. Differences in formaldehyde and acetaldehyde levels between filter-DNPH cartridges and the E-ACES were 14% ( p = 0.057) and 13% ( p = 0.380), respectively. The E-ACES showed reproducible nicotine and carbonyl testing results for the selected e-cigarette vaping conditions.