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Objective The objective of this study was to determine the incidence and predictors of intraoperative hypoxaemia and bradycardia in paediatric patients.Study design and setting A single-arm prospective cohort study was conducted, and data collection was carried out from 15 February 2024 to 30 September 2024 at Wachemo University, Nigest Elleni Mohammed Memorial Comprehensive Specialised Hospital.Participants The study included all paediatric patients undergoing surgery who had American Society of Anaesthesiologists classes II and III.Primary outcome measures Incidence and predictors of intraoperative hypoxaemia.Secondary outcome measures Incidence and predictors of intraoperative bradycardia.Results The incidence of intraoperative hypoxaemia was 33.3%. Paediatric age (<1 year), presence of comorbidities, use of muscle relaxants, use of narcotics and duration of surgery (≥1 hour) were predictors of intraoperative hypoxaemia, with p<0.005 and adjusted OR values of 5.3 (2.1–6.1), 4.1 (1.91–5.34), 3.1 (1.1–5.31), 4.01 (2.5–7.1) and 3.2 (1.41–6.1), respectively. However, the type of surgery was not associated with intraoperative hypoxaemia (p=0.081).This study has been conducted in a resource-limited setting and with methodological limitations such as short follow-up period, employing a single-arm cohort design, utilisation of sub-standardised intraoperative vital sign monitoring, proper intraoperative event documentation, over-reporting and under-reporting of the findings. This can cause overestimation of the incidence of hypoxaemia compared with studies conducted in a good resource set-up.Conclusion The incidence of intraoperative hypoxaemia and bradycardia, which is significantly associated with comorbidities, age (<1 year), use of opioids and muscle relaxants and surgeries lasting >1 hour, is high in paediatric patients who undergo surgery with general anaesthesia.Research registration Research registration unique identifying number (UIN) 10811 ( https://www.researchregistry.com).