This work aims to validate the Polar H7 heart rate (HR) sensor for heart rate variability (HRV) analysis at rest and during various exercise intensities in a cohort of male volunteers with different age, body composition and fitness level. Cluster analysis was carried out to evaluate how these phenotypic characteristics influenced HR and HRV measurements. For this purpose, sixty-seven volunteers performed a test consisting of the following consecutive segments: sitting rest, three submaximal exercise intensities in cycle-ergometer and sitting recovery. The agreement between HRV indices derived from Polar H7 and a simultaneous electrocardiogram (ECG) was assessed using concordance correlation coefficient (CCC). The percentage of subjects not reaching excellent agreement (CCC > 0.90) was higher for high-frequency power (PHF) than for low-frequency power (PLF) of HRV and increased with exercise intensity. A cluster of unfit and not young volunteers with high trunk fat percentage showed the highest error in HRV indices. This study indicates that Polar H7 and ECG were interchangeable at rest. During exercise, HR and PLF showed excellent agreement between devices. However, during the highest exercise intensity, CCC for PHF was lower than 0.90 in as many as 60% of the volunteers. During recovery, HR but not HRV measurements were accurate. As a conclusion, phenotypic differences between subjects can represent one of the causes for disagreement between HR sensors and ECG devices, which should be considered specifically when using Polar H7 and, generally, in the validation of any HR sensor for HRV analysis.