This chapter summarizes the research relating to microbiota, faecal transplants and pharmaceutical approaches in Functional gastrointestinal disorders (FGIDs). It provides practical recommendations in relation to these new approaches in managing functional gastrointestinal disorders. The gut microbiome is emerging as a key player in driving several peripheral and central mechanisms implicated in irritable bowel syndrome (IBS), including microbiota-gut-brain signalling, gastrointestinal motility, visceral hypersensitivity and epithelial barrier dysfunction. Therapeutic approaches directed at the gut microbiota include broad dietary interventions, specific dietary substances, prebiotics, live biotherapeutic products, antibiotics and microbial community interventions, such as faecal microbiota transplant. Serotonergic agents alosetron and ondansetron effectively treat IBS-D. Ramosetron is a potent and selective 5-HT3 receptor antagonist effective in improving stool consistency and other outcome measures in IBS-D patients. Overall, serotonergic pathway modulation continues to remain attractive in treatment of FGIDs and is of interest for future drug development.