Neonatal apnoea has been treated with caffeine, affecting the central nervous and the cardiovascular system. Heart rate variability (HRV) reflects the activity of the autonomic nervous system (ANS) and might be used as a measure of ANS maturation in newborns. We aimed to establish the effect of caffeine on HRV in newborns and sought for a potential correlation between HRV and the postmenstrual age. In 25 newborns hospitalized due to apnoea and treated with caffeine (2.5 mg/kg), we assessed breathing frequency, arterial oxygen saturation, body temperature, and the heart rate, while they were sleeping. We assessed HRV by spectral analysis using fast Fourier transformation. The same protocol was reapplied 100 hours after caffeine withdrawal to assess control parameters. Caffeine increased breathing frequency (p=0.023) but did not affect any other parameter assessed including HRV. We established a positive correlation between postmenstrual age and HRV during treatment with caffeine as well as after caffeine had been withdrawn (total power: p=0.044; low-frequency band: p=0.039). Apparently, the maintenance dose of caffeine is too low to affect the heart rate and the HRV. A positive correlation between postmenstrual age and HRV might reflect maturation of ANS, irrespective of caffeine treatment.