Pulmonary hypertension (PH) is a common finding that can result from many different pathological conditions. Depending on the etiology, treatment may be quite different, but early diagnosis and correct classification of PH is difficult. With an aging population and recently suggested decreased pulmonary arterial pressure threshold defining PH, we are facing even more diagnostic uncertainties. A new approach to patients’ phenotyping is needed. Here we present available data and future perspectives on employing an in-depth analysis of the omics cascade to allow an earlier and more reliable diagnosis and classification of PH. Indeed, with the help of super-fast computing, it became possible to simultaneously consider the levels of thousands of potential biomarkers to find patterns specific for clinically suspected disease. The omics cascade is an invaluable source of information. However, while the genome can be perceived as providing possibilities, transcriptome–as carving them this is metabolome that may tell us “what is really going on” in an individual living organism. Metabolomics research requires blinded search for characteristic patterns of discreet changes in the levels of detectable metabolites. Since as many as 40,000 various substances are produced as a “side effect of staying alive”, metabolite profiling can be compared to fishing up for organized signals in a universe of chaos. Although difficult, such search for metabolic patterns that might lead to replacing the term biomarker by metabolic fingerprinting in the area of pulmonary circulation has already begun.