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Background It is suggested that late initiation of toilet training contributes to functional gastrointestinal disorders in children. This study aims to evaluate if assisted infant toilet training can reduce the prevalence of functional gastrointestinal disorders during the first 9 months of life.Methods The ongoing Bowel And Bladder function in Infant Toilet Training (BABITT) study is a randomised, controlled trial that recruited infants aged 0–2 months at six Child Health Centres in Sweden. Infants were randomly assigned (1:1) to either start parent-assisted infant toilet training at the age of 0–2 months (intervention) or as controls. The intervention group was encouraged to practise at a moderate frequency of 1–3 times/day, 5–7 days/week. A validated web questionnaire was answered at ages 2, 3, 6 and 9 months.Results 271 infants (145 males, 54%) were randomly assigned at median age of 34 days (136 intervention; 135 controls). The intention-to-treat analysis with complete cases (127 intervention; 132 controls) showed no difference in the total period prevalence of functional gastrointestinal disorders (infant colic, infant dyschezia and/or functional constipation, defined by Rome IV criteria) between the intervention group and controls (52.0% vs 49.6%, difference 2.4% (95% CI −9.8 to 14.7); p=0.6956) up to the age of 9 months. Parent-reported intervention adherence ranged between 53% and 63%.Conclusions This study does not support that assisted infant toilet training, practised at a moderate frequency, reduces the prevalence of gastrointestinal disorders during infancy. Long-term effects are being evaluated in the ongoing BABITT study up to the age of 4 years.Trial registration number NCT04082689.