Heart rate variability (HRV) in women has been related independently to endogenous sex hormones, hormone replacement therapy, menopause, menstrual cycle, body mass index (BMI), and physical conditioning. However, the joint influence of all these factors has not been reported. The present study describes the relation between circadian variation HRV and assesses its association with BMI, age, and menstrual cycle in healthy young women. A multivariable analysis was performed to estimate the predictive variables involved in SDNN, pNN50, and rMSSD profile, using the classification and regression tree (CART) and the logistic regression models. It was found that the first predictive variable was age, which divided women in two groups: >29.5 years old and <29.5 years old. In the case of the SDNN, the second predictive variable was BMI; the highest values were observed in women younger than 23 years old, with a BMI less than 19.82 kg/m2 and during the follicular phase of her menstrual cycle. For pNN50 and rMSSD the second predictive variable was menstrual cycle for women younger than 29.5 years old. Thus, in this group of women, age was a major determinant of cardiac autonomic nervous modulation followed by the BMI. HRV may be better understood using a multivariable analysis that could mimic physiological conditions.