The aim of this study was to assess if, during high frequency oscillation (HFO), a frequency of 10 or 15 Hz was associated with lower carbon dioxide levels. Twelve infants were recruited, median gestational age 27 weeks. All infants were studied at both frequencies, applied in random order and the carbon dioxide level checked after 30 minutes on each frequency. Carbon dioxide levels were lower in 10 of the 12 infants at 10 compared to 15 Hz (p < 0.004) and, in the study population, overall were significantly lower at 10 Hz (p < 0.05). The difference in paCO2 levels at the two frequencies, however, was small, thus these results suggest the clinician should rely primarily on changes in oscillatory amplitude, rather than frequency, to effect changes in carbon dioxide levels.