Aim: Evaluations of sacs and cremaster muscles associated with undescended testis (UT) have revealed a decrease in sympathetic, but an increase in parasympathetic tonuses. Since the low frequency/high frequency power ratio obtained through spectral analysis of heart rate variability (HRV) determines the sympatho-parasympathetic balance, the sympatho-parasympathetic balance as defined by HRV in healthy boys and in boys with UT were compared. Material and methods: Sixteen healthy boys and 21 boys with UT presenting as an isolated anomaly were evaluated. Powers in low and high frequency bands were determined by spectral analysis, and low frequency/high frequency ratios were calculated. Data were compared by analysis of variance, and p-values less than 0.05 were considered significant. Results: Age distribution in the groups was similar. Low frequency/high frequency ratios were 2.27±1.84 and 1.26±0.79 in healthy boys and in boys with UT, respectively (p=0.0087). Conclusion: The autonomic balance is shifted with a decrease in sympathetic and an increase of parasympathetic tonus in boys with UT. This difference in signaling may help to understand the decrease in fertility, and the increase in the risk of malignancy in men with UT. © Georg Thieme Verlag KG Stuttgart - New York.