OBJECTIVE: In this study we investigated the relationship between heart rate variability (HRV) and respiration in healthy and probably asphyxiated infants using magnetocardiographic (MCG) recordings. METHODS: Ten healthy and eight infants from pregnancies complicated by preeclampsia with indications of mild perinatal asphyxia were included in the study. All were near term. Maternal age ranged from 16 to 39 years (mean = 29.05, SD = 6.13). Spectral analysis was used to find out any association between respiration and HRV. RESULTS: Respiratory sinus arrhythmia (RSA) was reduced in preeclamptic infants with indications of mild perinatal asphyxia. This difference was statistically significant (p < 0.0002, t-test), whereas the heart rate of the two groups was not statistically significant (p = 0.1, t-test). CONCLUSION: The results suggest that infants with indications of mild preeclampsia differ from controls in respiratory activity and this difference is independent of basal heart rate. Thus, spectral analysis could be useful for the estimation of influence of mild perinatal asphyxia in the RSA rhythm of newborns.