Spurred by recent events, there is an ever‐growing interest in the detection of volatile metabolites through human breath. Breath analysis, which is entirely noninvasive, can be applied to clinical diagnosis and therapeutic monitoring, where frequent sampling is required. The history of breath analysis can be traced back to as early as the time of ancient Greek. While the benefits of breath analysis are attractive, its technical basis and implementation are challenging. Despite the countless efforts in making use of breath analysis to guide clinical decisions, the potential of breath analysis remains to be fully exploited. The instruments used for breath analysis must be very selective, sensitive, and comprehensive. Comparing the published literature of several other mass spectrometry (MS)‐based breath analysis techniques, this review paper particularly focused on one recently developed breath analysis technique, secondary electrospray ionization mass spectrometry (SESI‐MS). SESI‐MS has major advantages such as its high ionization efficiency and its flexibility comparing to other existing techniques, as it can be interfaced with high‐end commercial mass spectrometers. In this review, the instrumentation, mechanism of ionization and extensive applications of SESI‐MS are discussed in detail.