Globally, diarrhoea is among the top five causes of mortality and morbidity among children under 5 years of age. It is one of the leading reasons children are brought to general practitioners and emergency departments for healthcare in high-income countries and imposes a significant clinical and cost burden. Acute gastroenteritis (AGE), an infectious intestinal disease which manifests mostly as diarrhoea and/or vomiting, is caused by viruses, bacteria, and protozoa. A wide range of micro-organisms can be detected in stool samples with polymerase chain reaction (PCR) assays but there is a lack of rigorously collected evidence to prove their pathogenicity. Vaccination for rotavirus has been introduced in Australia in 2007, and new vaccines for other micro-organisms are under development. There is a need to provide improved local indicators of epidemiology and pathogenicity for a range of organisms to develop future public health interventions. This Thesis aims to add to our understanding of the incidence, burden, and causes of gastrointestinal infections in healthy infants in a high-income setting during the first 2 years of life, including factors that may influence infection and the timing of the initial infection.