With its high molecular complexity, human breath lends itself as an information-rich sample for non-invasive biomedical diagnostics. Among emerging multi-variate analytical techniques for human breath, laser-based optical spectroscopy constitutes a particularly promising novel combination of short measurement times and high concentration dynamic range for molecular detection. Here, we present an automated system designed for continuous collection of exhaled breath directly from a respirator, and subsequent spectroscopic analysis. By obviating any additional intermediate sample storage or transport, our method minimizes setup complexity and sample contamination, while avoiding interference with the operation of the respirator. In this proof-of-principle study, we present automated and quantitative monitoring of three substances introduced in an artificial test lung ventilated by the respirator. Employing a standard Fourier-transform infrared spectrometer for molecular quantification, individual measurements were performed every 7 min over 24 h. The stability and analytical capability of the breath sampling system presented here, along with improvements in terms of spectral resolution and detection dynamic range obtainable through state-of-the-art laser-based spectroscopy promise fast and quantitative monitoring of the human breath volatilome. Coupled to state-of-the-art spectroscopy this may pave the way to monitor metabolites in real time in critically ill patients over the entire physiologically relevant molecular concentration range.