Perchlorate is regarded as an emerging persistent inorganic contaminant. It is widely known that perchlorate is an endocrine disruptor as it competitively inhibits iodide transport in the thyroid gland. As drinking water is the major source of human exposure to perchlorate, its occurrence in commercially available bottled waters purchased in different regions of Italy was investigated. Perchlorate was measured using the rapid, sensitive, and selective LC-ESI-MS/MS (liquid chromatography-electrospray tandem mass spectrometry) method by multiple reaction monitoring (MRM) of the transition 98.8→82.8, which corresponds to the loss of one oxygen atom in the perchlorate ion (ClO4−
). The chlorine isotope ratio (35
Cl) was used as a confirmation tool. The limit of quantification (LOQ) for this method was 5 ng/L, and the recovery ranged from 94% to 108%. Perchlorate was detected in 44 of the 62 drinking waters tested, with concentrations ranging from <5 to 75 ng/L. These values are similar in magnitude to those reported in drinking water from the USA and do not pose an immediate health concern.