Ageing is associated with changes in cardiac autonomic control as measured by Heart Rate Variability (HRV). Not many studies have explored the influence of gender on age-related changes in cardiac autonomic regulation. This study evaluated the gender differences in age-associated changes in cardiac autonomic nervous activity by assessing HRV using frequency domain analysis of short-term stationary R-R intervals. HRV was studied in healthy males and females ranging in age from 6 to 55 years. Total power and absolute power in High-Frequency (HF) and Low-Frequency (LF) components as well as HF in normalized unit declined significantly with ageing. The HF/LF ratio was significantly higher in the adolescent and adult females compared to male of these age groups. This study suggests that gender differences exist in age-related changes in HRV. The finding that gender differences are limited to adolescent and adult age groups may indicate a role for female sex hormones in cardiac autonomic modulation.