The use of electronic cigarettes (E-cig) is popular because of the perception that they are less addictive and safer compared to the traditional cigarettes. Nevertheless, there are still harmful effects associated with chemicals emitted from E-cig. Identifying the sources of the emitted compounds can be challenging because of the differences in the design of E-cig devices and the variability in the composition of E-cig liquids used in these devices. In this study, the emission profiles from impurity-free E-liquids containing only propylene glycol and glycerol in various percentage ratios along with two commercially available E-liquids were evaluated using gas chromatography–mass spectrometry (GC–MS). This study approach allows the elucidation of the transformation pathways of the major emitted compounds without the confounding effects of existing impurities or flavor ingredients added to E-liquids. Analysis of the vapor phases of E-cig emissions detected toxicants such as acetaldehyde, acrolein, benzaldehyde, as well as benzene, toluene, ethylbenzene, and xylene (BTEX) compounds. The amount of glycerol in the E-liquids has a major effect on the concentration of these hazardous compounds emitted because the concentration of these chemicals increased with increasing glycerol percentage in the E-liquid. Acetaldehyde and acrolein increased by 175-fold and 28-fold, respectively, when the glycerol composition was increased from 0 to 80%. Benzaldehyde, naphthalene, diphenyl ether, and glycerol along with menthol and nicotine that were present in the commercial E-liquids were also detected in the aerosol condensates. The cascade impactor data on the distribution of the nicotine and menthol in different size fractions from >2.5 to <2.5 μm allow the estimates of the extent of toxicant deposition in different parts of the pulmonary system including the oropharynx region, the trachea as well as inside the alveoli and bronchioles. In summary, users of E-cig are exposed to harmful chemicals even if the E-liquids contain only propylene glycol and glycerol without flavorings, nicotine, or impurities. Furthermore, this study shows that E-liquids containing higher percentages of glycerol will produce higher levels of toxicants compared to E-liquids with similar percentages of propylene glycol. This finding has important implications to E-cigarette vendors and manufacturers, consumers, and regulatory agencies.