"The development of Next Generation Sequencing (NGS) methods has enabled a precise identification of the enteric flora in humans and animals, partly owing to a 16S (bacterial small subunit ribosomal DNA) strategy. However, our insight into eukaryotic endobiotic organisms remains relatively limited. Molecular biological studies of genomic DNA extracted from faecal samples have given us an idea of the diversity among parasites and yeasts present in the human intestinal tract. This knowledge is necessary in order to expand on our understanding of the evolution, ecology and, perhaps most importantly, clinical significance of intestinal eukaryotic organisms, many of which may colonise the host for months or even years, and to evaluate our ability to detect them using current state-of-the-art methods. This insight is, however, still reached primarily by PCR and dideoxy-/Sanger sequencing despite the many limitations of this technology.To date, there have been no studies employing NGS methods for the investigation of the diversity of endobiotic eukaryotes. This is probably partly due to the fact that a broad 18S strategy – similar to the 16S strategy – involves unwanted amplification of human DNA. However, at the Laboratory of Parasitology, Statens Serum Institut, we have developed an 18S PCR method, which avoids amplification of human DNA. This means that PCR products can be analysed using NGS technology and bioinformatics tools without spending resources on data which have no or little interest. We now wish to validate and use this method to investigate the diversity of the human, eukaryotic enteric flora from different cohorts, including patients with inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), non-IBD/non-IBS diarrhoea and healthy individuals. The results are expected to have a vast impact on the clinical and diagnostic management of intestinal endosymbionts, and to assist in further clarifying the role of these organisms in health and disease."