Breath gas contains several hundreds of volatile organic compounds (VOCs) which are products of metabolic pathways and can be used to characterise the metabolic status e.g. during the development of metabolic disorders such as diabetes and obesity. In the German Mouse Clinic (GMC) mouse models for human diseases are characterised to understand molecular mechanisms of human disorders and for the development of new therapies. Mouse mutants with disorders in energy balance regulation are of special interest. Here, indirect calorimetry is the primary screening tool determining energy expenditure by gas exchange recording (i.e. O2 consumption and CO2 production). In the primary screen of the GMC, we plan to combine both indirect calorimetry and the measurement of VOCs in the breath gas using PTR-MS. For the online implementation of hs-PTR-MS, special conditions have to be considered regarding contaminations from bedding material, diet, faeces und urine. We demonstrate that head space analysis of these environmental confounders can be used to monitor disturbing effects interfering with VOCs in mouse breath gas. With a simple setup, consisting of a small box which is repeatedly flushed with clean synthetic air and continuously measuring the head space by hs-PTR-MS the crop up of urine and faeces can be clearly identified by distinct marker signals. Changes in breath frequency of mice during rest and activity are monitored by fluctuations in humidity in the head space volume. Implications of these monitoring conditions on the true VOCs of the breath gas of mice will be discussed in detail.