Coeliac disease is a condition that affects about one percent of the population, while non coeliac gluten sensitivity may affect up to a further 10% of the population. There is no current treatment for either of these conditions other than strict adherence to a life-long gluten-free diet. The current methods for measurement involve the use of antibody-based techniques including ELISA, but these approaches have some shortcomings. The use of ELISA to measure hydrolysed gluten, as present in fermented products such as beer, is a topic of hot debate. Liquid chromatography mass spectrometry (LC-MS) analysis has been introduced with an aim to develop quantitative markers for detection of the presence/absence and quantification of gluten in a diverse range of food matrices. We present our recent findings using LC-MS to detect hydrolysed gluten in gluten-free and gluten-reduced beers that are labelled as <20 ppm as judged by ELISA. LC-MS analyses revealed the presence of gluten peptides derived from hydrolysed gluten fragments, many of which were >30 kDa in size. Peptides representing all classes of hordein were detected in the conventional beers, but also alarmingly in several of the gluten-reduced beers. In a barley-based beer brewed from an ultra-low-gluten variety of barley, only a single gluten isoform known to be present was detected. The presence of large protein fragments in the gluten-reduced beers after prolyl endoprotease (PEP) treatment and/or proprietary processing are a cause for concern for those people with Coeliac disease as they may contain immunopathogenic sequences that could elicit adverse reactions.