In this article, technical developments in breath analysis and its applications in the field of clinical diagnosis and the monitoring of various symptoms, particularly molecular hydrogen in breath, are introduced. First, a brief overview of the current uses of the hydrogen breath test is provided. The principles of the test and how hydrogen can be used as a biomarker for various symptoms, and monitoring microbial metabolism, are introduced. Ten case-study applications of breath hydrogen measurements for which hydrogen exhibits beneficial effects for diagnosis, including the contexts of oxidative stress, gastrointestinal disease, and metabolic disorders, are discussed. The technologies and problems involved in breath hydrogen testing, sampling, pretreatment, and detection in exhaled breath are discussed, and research including current analytical systems and new sensors is focused on in the context of hydrogen detection.