During positive pressure ventilation, arterial pressure variations, like the pulse pressure variation (PPV), are observed in neonates. However, the frequency of the PPV does not always correspond with the respiratory rate. It is hypothesized that PPV is caused by cardiopulmonary interaction, but that this mismatch is related to the low respiratory rate/heart rate ratio. Therefore, the goal of this study is to investigate the relation between PPV and ventilation in neonates. A prospective observational cross-sectional study was carried out in a third-level neonatal intensive care unit in a university hospital. Neonates on synchronized intermittent mandatory ventilation (SIMV) or high-frequency ventilation (HFV) participated in the study. The arterial blood pressure was continuously monitored in 20 neonates on SIMV and 10 neonates on HFV. In neonates on SIMV the CO2 waveform and neonates on HFV the thorax impedance waveform were continuously monitored and defined as the respiratory signal. Correlation and coherence between the respiratory signal and pulse pressure were determined. The correlation between the respiratory signal and pulse pressure was -0.64 ± 0.18 and 0.55 ± 0.16 and coherence at the respiratory frequency was 0.95 ± 0.11 and 0.76 ± 0.4 for SIMV and HFV, respectively. The arterial pressure variations observed in neonates on SIMV or HFV are related to cardiopulmonary interaction. Despite this relation, it is not likely that PPV will reliably predict fluid responsiveness in neonates due to physiological aliasing.