Our aim is to demonstrate the usefulness of photoplethysmography (PPG) for analyzing heart rate variability (HRV) using a standard 5-min test at rest with paced breathing, comparing the results with real RR intervals and testing supine and sitting positions. Simultaneous recordings of R-R intervals were conducted with a Polar system and a non-contact PPG, based on facial video recording on 20 individuals. Data analysis and editing were performed with individually designated software for each instrument. Agreement on HRV parameters was assessed with concordance correlations, effect size from ANOVA and Bland and Altman plots. For supine position, differences between video and Polar systems showed a small effect size in most HRV parameters. For sitting position, these differences showed a moderate effect size in most HRV parameters. A new procedure, based on the pixels that contained more heart beat information, is proposed for improving the signal-to-noise ratio in the PPG video signal. Results were acceptable in both positions but better in the supine position. Our approach could be relevant for applications that require monitoring of stress or cardio-respiratory health, such as effort/recuperation states in sports.