The cardiac sympathetic nervous system is one putative key factor involved in the intrauterine programming of adult cardiovascular disease. We therefore analyzed the cardiac autonomic system activity in small for gestational age (SGA) neonates. Heart rate variability (HRV) from 24h electrocardiographic (ECG) recordings were analyzed for time domain and frequency domain parameters in 27 SGA neonates (median 261 (240-283) days of gestation) and compared to 27 appropriate for gestational age (AGA) neonates (median 270 (239-293) days of gestation). In addition, salivary α-amylase levels were analyzed during resting conditions and in response to a pain induced stress event in 18 SGA (median 266 (240-292) days of gestation) and 36 AGA (median 271 (240-294) days of gestation) neonates. Overall HRV was not significantly different in SGA compared to AGA neonates (SDNN: p=0.14; triangular index: p=0.29) and sympathovagal balance (LF/HF) was similar (p=0.62) Parameters mostly influenced by sympathetic activity did not reveal significant differences: (SDANN: p=0.27; SDNNi: p=0.66, LF: p=0.83) as well as vagal tone influenced parameters were unaltered (r-MSSD: p=0.59; pNN50: p=0.4; HF: p=0.82). Median resting levels for -amylase were not significantly different in SGA neonates (p=0.13) and a neonatal stress stimulus revealed similar stress response patterns (p=0.29). HRV and salivary -amylase levels as indicator of cardiac autonomic activity are not altered in SGA compared to AGA neonates. Thus, it appears that intrauterine activation of the sympathetic system in SGA fetuses does not directly persist into postnatal life and neonatal sympatho-vagal balance appears to be preserved.