Breath analysis has great potential for becoming an important clinical diagnosis method due to its friendly and non-invasive way of sample collection. Hundreds of endogenous trace gases (volatile organic compounds (VOCs)) are present in breath, representing different metabolic processes of the body. They are not only characteristic for a person, their age, sex, habit etc, but also specific to different kinds of diseases. VOCs, related to diseases could serve as biomarkers for clinical diagnostics and disease monitoring. However, due to the large amount of water contained in breath, an identification of specific VOCs is a real challenge. In this work we present a technique of water suppression from breath samples, that enables us to identify several trace gases in breath, e.g., methane, isoprene, acetone, aldehyde, carbon monoxide, etc, using Fourier-transform infrared spectroscopy. In the current state, the technique reduces the water concentration by a factor of 2500. Sample preparation and data acquisition take about 25 min, which is clinically relevant. In this article we demonstrate the working principle of the water reduction technique. Further, with specific examples we demonstrate that water elimination from breath samples does not hamper the concentration of trace gases in breath. Preliminary experiments with real breath also indicate that the concentrations of methane, acetone and isoprene remain the same during the sample preparation.