Effective functioning of the gastrointestinal (GI) tract is essential for determining and sustaining animal health, welfare and performance. A balanced diet, efficient digestion and absorption, normal and stable microbiota, a robust immune system, and a healthy gut mucosa are the primary key components determining optimal GI functionality. These pivotal factors offer an opportunity to explore potential biomarkers for evaluating the performance of the GI system in animals. Among various biological samples, faecal samples emerge as advantageous due to their easy collection, non-invasiveness, applicability in wild animals, minimum stress, and their contribution to animal welfare. While literature on faecal biomarkers in animals is scarce, some studies have investigated such indicators in monogastric, wild, and laboratory animals; these include lactate and succinate (indicators of fermentative diarrhoea), sialic acid (indicative of intestinal damage), glucocorticoid (stress marker), intestinal alkaline phosphatase (associated with pathogenic intestinal damage), and lipocalin-2 and calprotectin (indicating intestinal inflammation). Faecal glucocorticoid metabolites are particularly useful for evaluating environmental or captive stress in wild animals. The aforementioned faecal biomarkers offer insights into events influencing GI functionality and may pave the way for developing nutritional interventions aimed at modulating the GI system to enhance animal welfare and performance.