Neonatal heart rate and its interaction with respiration were computerized by spectral and coherence analysis (FFT) to differentiate healthy newborns (n = 9) from newborns with mild neonatal risk (n = 20). An increased mean heart rate and decreased total variability have been found in newborns-at-risk. Respiratory Sinus Arrhythmia is diminished in newborns-at-risk possibly caused by an impairment of autonomic brain stem function. Furthermore, Respiratory Sinus Arrhythmia holds a central position in differentiating healthy newborns and newborns-at-risk with and without neurological abnormalities during the first year of life. Respiratory Sinus Arrhythmia is diminished in newborns-at-risk showing these abnormalities. None of the parameters discriminates between the two groups of risk infants. The final prognostic value of our results must be confirmed in further clinical follow-up examinations.