The most common problems that paediatricians and paediatric gastroenterologists encounter in their practice include functional gastrointestinal disorders. These are a group of chronic and/or recurrent conditions caused by any combination of gastrointestinal motility disturbances and visceral hypersensitivity with abnormal processing of stimuli in the central nervous system which manifest with abdominal pain, nausea and vomiting or disorders of defecation, among other problems. The symptoms cannot be assigned to any other clinical condition despite proper diagnostic investigation. The aetiology of functional gastrointestinal disorders is multifactorial. Recently, the role of the intestinal microbiota as an important environmental factor in the pathogenesis of such disorders has been investigated. In this article, the latest data regarding the composition of the microbiome (a collection of microbiota genes) of the human gastrointestinal tract are discussed and the methods used to determine it in detail are described. Currently, molecular biology techniques have the highest diagnostic value, which are based on genetic material sequencing. Due to their extraordinary efficacy, they are superseding classic microbiological tests. In addition, the publication presents factors which affect the composition of the gastrointestinal microbiome. These include, for example, mode of birth, method of infant feeding, diet at later stages of life, place of residence, physical activity and antibiotics intake. The research to date demonstrated that dysbiosis is one of the factors contributing to the pathogenesis of many diseases, including irritable bowel syndrome. Attempts at modifying the composition of the microbiome by, for example, the administration of probiotics, should therefore have a distinctly positive effect on patients with functional gastrointestinal disorders.