Exhaled breath contains thousands of volatile organic compounds (VOCs) of which the composition varies depending on health status. Various metabolic processes within the body produce volatile products that are released into the blood and will be passed on to the airway once the blood reaches the lungs. Moreover, the occurrence of chronic inflammation and/or oxidative stress can result in the excretion of volatile compounds that generate unique VOC patterns. Consequently, measuring the total amount of VOCs in exhaled air, a kind of metabolomics also referred to as breathomics, for clinical diagnosis and monitoring purposes gained increased interest over the last years. This paper describes the currently available methodologies regarding sampling, sample analysis and data processing as well as their advantages and potential drawbacks. Additionally, different application possibilities of VOC profiling are discussed. Until now, breathomics has merely been applied for diagnostic purposes. Exhaled air analysis can, however, also be applied as an analytical or monitoring tool. Within the analytic perspective, the use of VOCs as biomarkers of oxidative stress, inflammation or carcinogenesis is described. As monitoring tool, breathomics can be applied to elucidate the heterogeneity observed in chronic diseases, to study the pathogen(s) responsible for occurring infections and to monitor treatment efficacy.