Several studies have shown the presence of aldehydes (i.e., formaldehyde, acrolein) in mainstream emissions of some e-cigarettes. For this reason, concerns have been raised regarding potential toxicity. The purpose of this research was to measure levels of carbonyls in exhaled breath of e-cigarette users during “vaping” sessions and estimate the respiratory tract (RT) uptake of specific aldehydes, including formaldehyde and acetaldehyde. We measured concentrations of 12 carbonyls in e-cigarette aerosols produced directly by e-cigarettes and in the exhaled breath of 12 participants (19 sessions). Carbonyls were sampled on 2,4-dinitrophenylhydrazine (DNPH) cartridges and analyzed with high performance liquid chromatography (HPLC) coupled with a UV/Vis photodiode detector. We found that in most cases, levels of aldehydes and methyl ethyl ketone (MEK) were significantly higher (2–125 times) in exhaled e-cigarette breaths than in pre-exposed breath. Exposure levels for the most abundant individual carbonyls in e-cigarette emissions—formaldehyde, acetaldehyde, acrolein—were between the limit of quantification (LOQ) and 24.4 μg·puff −1. The mean retention of formaldehyde in the respiratory tract was 99.7 ± 0.9% for all participants, while acetaldehyde retention was 91.6 ± 9.9%. Within the limitation of a small number of participants, our results showed that there is an increase in breath carbonyls during e-cigarette use.