Heart Rate Variability (HRV), the variation of time intervals between heartbeats, is one of the most promising and widely used quantitative markers of autonomic activity. Traditionally, HRV is measured as the series of instantaneous cycle intervals obtained from the electrocardiogram (ECG). In this study, we investigated the estimation of variation in heart rate from a photoplethysmography (PPG) signal, called pulse rate variability (PRV), and assessed its accuracy as an estimate of HRV in children with and without sleep disordered breathing (SDB). We recorded raw PPGs from 72 children using the Phone Oximeter, an oximeter connected to a mobile phone. Full polysomnography including ECG was simultaneously recorded for each subject. We used correlation and Bland-Altman analysis for comparing the parameters of HRV and PRV between two groups of children. Significant correlation (r > 0.90, p < 0.05) and close agreement were found between HRV and PRV for mean intervals, standard deviation of intervals (SDNN) and the root-mean square of the difference of successive intervals (RMSSD). However Bland-Altman analysis showed a large divergence for LF/HF ratio parameter. In addition, children with SDB had depressed SDNN and RMSSD and elevated LF/HF in comparison to children without SDB. In conclusion, PRV provides the accurate estimate of HRV in time domain analysis but does not reflect precise estimation for parameters in frequency domain.