The assessment of disease activity in various conditions may be performed using a range of different techniques. These include the use of non-invasive tests, such as acute phase inflammatory markers and simple radiological techniques, to more advanced invasive and complex modalities. Over the past two decades the analysis of volatile organic compounds (VOCs) in biological specimens has attracted a considerable amount of clinical interest. The investigation of VOCs, using a variety of analytical techniques, has shown a significant correlation between the pattern and concentration of VOCs and the occurrence of various diseases. This provides a potentially non-invasive means of diagnosis, monitoring of pathological processes and assessment of pharmacological response. It may be rapid, simple and acceptable to patients. In this paper we review the medical literature and research efforts that have been carried out over the past decades, and try to summarize the clinical implications of VOC analysis of various biological emanations including stool, breath and blood samples and their correlation with gastrointestinal and liver diseases.