Atelectasis occurs commonly during induction of general anaesthesia in children, particularly infants. We hypothesised that maintaining spontaneous ventilation can reduce atelectasis formation during anaesthetic induction in infants. We compared spontaneous ventilation and manual positive-pressure ventilation in terms of atelectasis formation in infants. Randomised controlled study. Single tertiary hospital in Seoul, Republic of Korea, from November 2018 to December 2019. We enrolled 60 children younger than 1 year of age undergoing general anaesthesia, of whom 56 completed the study. Exclusion criteria were history of hypoxaemia during previous general anaesthesia, development of a respiratory tract infection within 1 month, current intubation or tracheostomy cannulation, need for rapid sequence intubation, preterm birth, age within 60 weeks of the postconceptional age and the presence of contraindications for rocuronium or sodium thiopental. Patients were allocated randomly to either the 'spontaneous' group or 'controlled' group. During preoxygenation, spontaneous ventilation was maintained in the 'spontaneous' group while conventional bag-mask ventilation was provided in the 'controlled' group. After 5 min of preoxygenation, a lung ultrasound examination was performed to compare atelectasis formation in the two groups. Atelectasis after preoxygenation was seen in seven (26.9%) of 26 patients in the 'spontaneous' group and 22 (73.3%) of 30 patients in the 'controlled' group (P = 0.001). The relative risk of atelectasis in the 'spontaneous' group was 0.39 (95% CI 0.211 to 0.723). Regarding ultrasound pictures of consolidation, the total score and sum of scores in the dependent regions were significantly lower in the 'spontaneous' group than in the 'controlled' group (P = 0.007 and 0.001, respectively). Maintaining spontaneous ventilation during induction of general anaesthesia has a preventive effect against atelectasis in infants younger than 1 year of age, particularly in the dependent portions of the lungs. Clinicaltrials.gov (identifier: NCT03739697).