Measuring heart rate variability (HRV) is widely used to assess autonomic nervous system function. It requires accurate measurement of the interval between successive heartbeats. This can be achieved from recording the electrocardiogram (ECG), which is non-invasive and widely available. However, methodological problems inherent in recording and analyzing ECG traces have motivated a search for alternative means of measuring the interval between successive heartbeats. Recording blood oxygenation pulsations (photoplethysmography-PPG) is also convenient, non-invasive and widely available, and has been suggested as an effective alternative to ECG to derive HRV. Moreover, it has been claimed that the pulse waveforms produced by oximetry may be more practicable than R-R intervals measured from the by ECG, especially for ambulatory recordings. We have therefore compared PPG with ECG recordings to measure HRV applying the same signal analysis techniques to PPG and ECG recordings made simultaneously. Comparison of 5 min recording epochs demonstrated a very high degree of correlation, in temporal, frequency domains and non-linear analysis, between HRV measures derived from the PPG and ECG. However, we found that the PPG signal is especially vulnerable to motion artifacts when compared to the ECG, preventing any HRV analysis at all in a significant minority of PPG recordings. Our results demonstrate that even though PPG provides accurate interpulse intervals to measure heart rate variability under ideal conditions, it is less reliable due to its vulnerability to motion artifacts. Therefore it is unlikely to prove a practical alternative to the ECG in ambulatory recordings or recordings made during other activities.