The linear model-based multiscale complexity (MSC) approach allows the estimation of the cardiac control complexity over short heart period (HP) series (about 300 samples) at time scales linked to cardiac autonomic control, i.e. in the low frequency (LF, 0.05-0.15 Hz) and high frequency (HF, 0.15-0.4 Hz) bands. As far as the cardiac control is concerned, a few studies assessed gender differences. We hypothesize that the application of MSC to HP variability could provide important insights about gender differences. The aim of this study was to compare complexity of the cardiac control in females and males via MSC analysis of HP variability. Twenty-three healthy females (WOMEN, age 36±6 yrs) and twenty-one males (MEN, age 35±5 yrs) underwent standard 24-hour Holter electrocardiogram. MSC analysis was performed over sequences of 300 consecutive HP values. Indexes of the overall complexity (CI) and of complexity in the LF and HF bands (CILF and CIHF respectively) were derived. Power spectral markers were computed as well. Analyses were iterated (with 80% overlap) over series of 2500 HP values selected during daytime (DAY) and nighttime (NIGHT) and the median of the distribution of the resulting markers was derived. We found that power spectral indexes were similar in WOMEN and MEN, while during DAY CI and CILF were higher in WOMEN than MEN (0.31±0.09 vs 0.22±0.09 and 0.16±0.05 vs 0.14±0.05 respectively). No gender differences were detected during NIGHT. These results suggest that the CILF is responsible of a higher overall HP complexity in WOMEN. This finding could be the consequence of a lower sympathetic drive and a more complex hormonal regulation in WOMEN than MEN. We conclude that MSC was more powerful than power spectral analysis in detecting gender differences and this diversity might be fruitfully exploited to differentiate preventive and therapeutic interventions in WOMEN and MEN.