Early treatment by thyroid hormone in congenital hypothyroidism (CH) prevents for mental retardation, but the autonomic condition could well remain impaired. The aim of this study was to get insights about the cardiovascular regulation of CH children by analysing their heart rate variability (HRV) data. RR-interval data of 34 early treated CH children, 24 to 48 months of age, were collected at rest in a clinical environment. In all these cases, CH resulted from an abnormal development of thyroid gland. Data from 29 age matched-controls were also collected in a scholar environment. Short time series were then analysed in time and frequency domains. Detrended fluctuation analysis (DFA) was also applied to obtain the scaling exponent alpha(1). We found that the HRV obtained from children with CH is diminished as suggested by statistical differences (p<0.05) in the following parameters: RMSDD, pNN20, total power, LF and HF. However, no significant differences were found in the LF/HF ratio, the central frequencies of the LF and HF bands, as well as in alpha(1). Given that the significant differences were basically reflected in static parameters rather than in the frequency distribution or scale-invariant behaviour of the studied data, we consider that the analysis points toward the effect of treatment on rising heart rate by the thyroid hormone, and not necessarily toward any residual autonomic dysfunction, as the dominant underlying cause of the diminished HRV exhibited by CH children.