Objective - To determine reference values for oxygen saturation (SaO2) in healthy children younger than 5 years living at high altitude. Design - One hundred and sixty eight children were examined for SaO2 at 4018 m during well child visits. Physiological state was also noted during the examination. Results - The mean SaO2 was 87.3% (95% confidence intervals (CI) 86.7%, 87.9%) with a median value of 87.7%. A significant difference was observed in SaO2 between children younger than 1 year compared with older children, although the difference was no longer demonstrable when sleeping children were excluded. Conclusions - This study has provided a reference range of SaO2 values for healthy children under 5 years old so that pulse oximetry may be used as an adjunct in diagnosing acute respiratory infections. Younger children were also shown to have a lower mean SaO2 than older children living at high altitude, which suggests physiological adaptation to high altitude over time. In addition, sleep had a lowering effect on SaO2, although the clinical importance of this remains undetermined.