Gastrointestinal (GI) symptoms are common and can affect children's social lives. This study investigated the effects of exposure to a rich natural environment on GI symptoms, salivary cortisol levels, salivary amylase levels, and the gut microbiota in young children. Children aged 5-6 years from four kindergartens in Japan were randomly assigned to two groups: a nature childcare group and a regular childcare group. The children were exposed to their respective conditions once weekly for one month. Before and after the intervention, GI symptoms were detected using the Children's Somatization Inventory to calculate a 'GI score' and categorize participants into GI and control groups (primary outcome measure). Fecal examinations were performed for gut microbiota using 16 S-rRNA analysis, salivary cortisol and amylase levels were quantified, and the Child Behavior Checklist was administered. The two groups had similar GI symptoms, salivary cortisol and amylase levels, and behavioral characteristics. Following the intervention, significant differences in the GI score, abdominal pain, constipation, Shannon index value, and salivary cortisol and amylase levels (p <
0.05) were observed between the two childcare groups. Spending free and abundant time in nature during early childhood could help maintain digestive system homeostasis, increase gut microbiota diversity, and reduce cortisol levels.