The purpose of this study was the development of various analytical MS methods to investigate the chemical composition of e-liquids used in electronic cigarettes and characterize their quality. Low-quality nicotine (the main active compound), glycerol, propylene glycol (solvents), or flavors could greatly increase the toxicity. The search of alkaloid contaminants of nicotine was performed by LC–MS-MS after a deep study of fragmentation pathways by high resolution ESI-MS. A fully validated method for quantitation of organic polar impurities such as cotinine, anabasine, myosmine, nornicotine, and N-nitroso-nornicotine and nicotine itself was developed using MS coupled to UHPLC. To evaluate organic volatile toxicants, headspace from e-cigarette refill liquids was sampled by SPME to perform GC–MS analysis. Finally, heavy metal residues as inorganic toxicants were determined by ICP-MS after simple dilution. A number of cases of contamination by metals (mainly arsenic) was detected.